dragon-ml-toolbox 13.3.2__tar.gz → 13.5.0__tar.gz

{dragon_ml_toolbox-13.3.2/dragon_ml_toolbox.egg-info → dragon_ml_toolbox-13.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dragon-ml-toolbox
-Version: 13.3.2
+Version: 13.5.0
 Summary: A collection of tools for data science and machine learning projects.
 Author-email: "Karl L. Loza Vidaurre" <luigiloza@gmail.com>
 License-Expression: MIT

{dragon_ml_toolbox-13.3.2 → dragon_ml_toolbox-13.5.0/dragon_ml_toolbox.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dragon-ml-toolbox
-Version: 13.3.2
+Version: 13.5.0
 Summary: A collection of tools for data science and machine learning projects.
 Author-email: "Karl L. Loza Vidaurre" <luigiloza@gmail.com>
 License-Expression: MIT

{dragon_ml_toolbox-13.3.2 → dragon_ml_toolbox-13.5.0}/ml_tools/ML_datasetmaster.py

@@ -126,8 +126,8 @@ class _BaseDatasetMaker(ABC):
         else:
             _LOGGER.info("No continuous features listed in schema. Scaler will not be fitted.")
 
-        X_train_values = X_train.values
-        X_test_values = X_test.values
+        X_train_values = X_train.to_numpy()
+        X_test_values = X_test.to_numpy()
 
         # continuous_feature_indices is derived
         if self.scaler is None and continuous_feature_indices:
@@ -253,26 +253,42 @@ class DatasetMaker(_BaseDatasetMaker):
                  pandas_df: pandas.DataFrame,
                  schema: FeatureSchema,
                  kind: Literal["regression", "classification"],
+                 scaler: Union[Literal["fit"], Literal["none"], PytorchScaler],
                  test_size: float = 0.2,
-                 random_state: int = 42,
-                 scaler: Optional[PytorchScaler] = None):
+                 random_state: int = 42):
         """
         Args:
             pandas_df (pandas.DataFrame): 
                 The pre-processed input DataFrame containing all columns. (features and single target).
             schema (FeatureSchema): 
                 The definitive schema object from data_exploration.
-            kind (Literal["regression", "classification"]): 
+            kind ("regression" | "classification"): 
                 The type of ML task. This determines the data type of the labels.
+            scaler ("fit" | "none" | PytorchScaler): 
+                Strategy for data scaling:
+                - "fit": Fit a new PytorchScaler on continuous features.
+                - "none": Do not scale data (e.g., for TabularTransformer).
+                - PytorchScaler instance: Use a pre-fitted scaler to transform data.
             test_size (float): 
                 The proportion of the dataset to allocate to the test split.
             random_state (int): 
                 The seed for the random number of generator for reproducibility.
-            scaler (PytorchScaler | None): 
-                A pre-fitted PytorchScaler instance, if None a new scaler will be created.
+            
         """
         super().__init__()
-        self.scaler = scaler
+        
+        _apply_scaling: bool = False
+        if scaler == "fit":
+            self.scaler = None # To be created
+            _apply_scaling = True
+        elif scaler == "none":
+            self.scaler = None
+        elif isinstance(scaler, PytorchScaler):
+            self.scaler = scaler # Use the provided one
+            _apply_scaling = True
+        else:
+            _LOGGER.error(f"Invalid 'scaler' argument. Must be 'fit', 'none', or a PytorchScaler instance.")
+            raise ValueError()
         
         # --- 1. Identify features (from schema) ---
         self._feature_names = list(schema.feature_names)
@@ -310,9 +326,14 @@ class DatasetMaker(_BaseDatasetMaker):
         label_dtype = torch.float32 if kind == "regression" else torch.int64
 
         # --- 4. Scale (using the schema) ---
-        X_train_final, X_test_final = self._prepare_scaler(
-            X_train, y_train, X_test, label_dtype, schema
-        )
+        if _apply_scaling:
+            X_train_final, X_test_final = self._prepare_scaler(
+                X_train, y_train, X_test, label_dtype, schema
+            )
+        else:
+            _LOGGER.info("Features have not been scaled as specified.")
+            X_train_final = X_train.to_numpy()
+            X_test_final = X_test.to_numpy()
         
         # --- 5. Create Datasets ---
         self._train_ds = _PytorchDataset(X_train_final, y_train, labels_dtype=label_dtype, feature_names=self._feature_names, target_names=self._target_names)
@@ -336,9 +357,9 @@ class DatasetMakerMulti(_BaseDatasetMaker):
                  pandas_df: pandas.DataFrame,
                  target_columns: List[str],
                  schema: FeatureSchema,
+                 scaler: Union[Literal["fit"], Literal["none"], PytorchScaler],
                  test_size: float = 0.2,
-                 random_state: int = 42,
-                 scaler: Optional[PytorchScaler] = None):
+                 random_state: int = 42):
         """
         Args:
             pandas_df (pandas.DataFrame): 
@@ -348,20 +369,35 @@ class DatasetMakerMulti(_BaseDatasetMaker):
                 List of target column names.
             schema (FeatureSchema): 
                 The definitive schema object from data_exploration.
+            scaler ("fit" | "none" | PytorchScaler): 
+                Strategy for data scaling:
+                - "fit": Fit a new PytorchScaler on continuous features.
+                - "none": Do not scale data (e.g., for TabularTransformer).
+                - PytorchScaler instance: Use a pre-fitted scaler to transform data.
             test_size (float): 
                 The proportion of the dataset to allocate to the test split.
             random_state (int): 
                 The seed for the random number generator for reproducibility.
-            scaler (PytorchScaler | None): 
-                A pre-fitted PytorchScaler instance.
                 
         ## Note:
         For multi-binary classification, the most common PyTorch loss function is nn.BCEWithLogitsLoss. 
         This loss function requires the labels to be torch.float32 which is the same type required for regression (multi-regression) tasks.
         """
         super().__init__()
-        self.scaler = scaler
-
+        
+        _apply_scaling: bool = False
+        if scaler == "fit":
+            self.scaler = None
+            _apply_scaling = True
+        elif scaler == "none":
+            self.scaler = None
+        elif isinstance(scaler, PytorchScaler):
+            self.scaler = scaler # Use the provided one
+            _apply_scaling = True
+        else:
+            _LOGGER.error(f"Invalid 'scaler' argument. Must be 'fit', 'none', or a PytorchScaler instance.")
+            raise ValueError()
+        
         # --- 1. Get features and targets from schema/args ---
         self._feature_names = list(schema.feature_names)
         self._target_names = target_columns
@@ -403,9 +439,14 @@ class DatasetMakerMulti(_BaseDatasetMaker):
         label_dtype = torch.float32 
 
         # --- 4. Scale (using the schema) ---
-        X_train_final, X_test_final = self._prepare_scaler(
-            X_train, y_train, X_test, label_dtype, schema
-        )
+        if _apply_scaling:
+            X_train_final, X_test_final = self._prepare_scaler(
+                X_train, y_train, X_test, label_dtype, schema
+            )
+        else:
+            _LOGGER.info("Features have not been scaled as specified.")
+            X_train_final = X_train.to_numpy()
+            X_test_final = X_test.to_numpy()
         
         # --- 5. Create Datasets ---
         # _PytorchDataset now correctly handles y_train (a DataFrame)

{dragon_ml_toolbox-13.3.2 → dragon_ml_toolbox-13.5.0}/ml_tools/ML_evaluation.py

@@ -258,7 +258,7 @@ def shap_summary_plot(model,
                       feature_names: Optional[list[str]], 
                       save_dir: Union[str, Path],
                       device: torch.device = torch.device('cpu'),
-                      explainer_type: Literal['deep', 'kernel'] = 'deep'):
+                      explainer_type: Literal['deep', 'kernel'] = 'kernel'):
     """
     Calculates SHAP values and saves summary plots and data.
 
@@ -270,7 +270,7 @@ def shap_summary_plot(model,
         save_dir (str | Path): Directory to save SHAP artifacts.
         device (torch.device): The torch device for SHAP calculations.
         explainer_type (Literal['deep', 'kernel']): The explainer to use.
-            - 'deep': (Default) Uses shap.DeepExplainer. Fast and efficient for
+            - 'deep': Uses shap.DeepExplainer. Fast and efficient for
               PyTorch models.
             - 'kernel': Uses shap.KernelExplainer. Model-agnostic but EXTREMELY
               slow and memory-intensive.
@@ -285,7 +285,7 @@ def shap_summary_plot(model,
     instances_to_explain_np = None
 
     if explainer_type == 'deep':
-        # --- 1. Use DeepExplainer (Preferred) ---
+        # --- 1. Use DeepExplainer  ---
         
         # Ensure data is torch.Tensor
         if isinstance(background_data, np.ndarray):
@@ -309,10 +309,9 @@ def shap_summary_plot(model,
         instances_to_explain_np = instances_to_explain.cpu().numpy()
 
     elif explainer_type == 'kernel':
-        # --- 2. Use KernelExplainer (Slow Fallback) ---
+        # --- 2. Use KernelExplainer ---
         _LOGGER.warning(
-            "Using KernelExplainer. This is memory-intensive and slow. "
-            "Consider reducing 'n_samples' if the process terminates unexpectedly."
+            "KernelExplainer is memory-intensive and slow. Consider reducing the number of instances to explain if the process terminates unexpectedly."
         )
 
         # Ensure data is np.ndarray
@@ -348,14 +347,26 @@ def shap_summary_plot(model,
     else:
         _LOGGER.error(f"Invalid explainer_type: '{explainer_type}'. Must be 'deep' or 'kernel'.")
         raise ValueError()
+    
+    if not isinstance(shap_values, list) and shap_values.ndim == 3 and shap_values.shape[2] == 1:
+        # _LOGGER.info("Squeezing SHAP values from (N, F, 1) to (N, F) for regression plot.")
+        shap_values = shap_values.squeeze(-1)
 
     # --- 3. Plotting and Saving ---
     save_dir_path = make_fullpath(save_dir, make=True, enforce="directory")
     plt.ioff()
     
+    # Convert instances to a DataFrame. robust way to ensure SHAP correctly maps values to feature names.
+    if feature_names is None:
+        # Create generic names if none were provided
+        num_features = instances_to_explain_np.shape[1]
+        feature_names = [f'feature_{i}' for i in range(num_features)]
+        
+    instances_df = pd.DataFrame(instances_to_explain_np, columns=feature_names)
+    
     # Save Bar Plot
     bar_path = save_dir_path / "shap_bar_plot.svg"
-    shap.summary_plot(shap_values, instances_to_explain_np, feature_names=feature_names, plot_type="bar", show=False)
+    shap.summary_plot(shap_values, instances_df, plot_type="bar", show=False)
     ax = plt.gca()
     ax.set_xlabel("SHAP Value Impact", labelpad=10)
     plt.title("SHAP Feature Importance")
@@ -366,7 +377,7 @@ def shap_summary_plot(model,
 
     # Save Dot Plot
     dot_path = save_dir_path / "shap_dot_plot.svg"
-    shap.summary_plot(shap_values, instances_to_explain_np, feature_names=feature_names, plot_type="dot", show=False)
+    shap.summary_plot(shap_values, instances_df, plot_type="dot", show=False)
     ax = plt.gca()
     ax.set_xlabel("SHAP Value Impact", labelpad=10)
     if plt.gcf().axes and len(plt.gcf().axes) > 1:
@@ -389,9 +400,6 @@ def shap_summary_plot(model,
         mean_abs_shap = np.abs(shap_values).mean(axis=0)
 
     mean_abs_shap = mean_abs_shap.flatten()
-    
-    if feature_names is None:
-        feature_names = [f'feature_{i}' for i in range(len(mean_abs_shap))]
         
     summary_df = pd.DataFrame({
         SHAPKeys.FEATURE_COLUMN: feature_names,
@@ -401,7 +409,7 @@ def shap_summary_plot(model,
     summary_df.to_csv(summary_path, index=False)
     
     _LOGGER.info(f"📝 SHAP summary data saved as '{summary_path.name}'")
-    plt.ion()    
+    plt.ion()
 
 
 def plot_attention_importance(weights: List[torch.Tensor], feature_names: Optional[List[str]], save_dir: Union[str, Path], top_n: int = 10):

{dragon_ml_toolbox-13.3.2 → dragon_ml_toolbox-13.5.0}/ml_tools/ML_evaluation_multi.py

@@ -235,7 +235,7 @@ def multi_target_shap_summary_plot(
     target_names: List[str],
     save_dir: Union[str, Path],
     device: torch.device = torch.device('cpu'),
-    explainer_type: Literal['deep', 'kernel'] = 'deep'
+    explainer_type: Literal['deep', 'kernel'] = 'kernel'
 ):
     """
     Calculates SHAP values for a multi-target model and saves summary plots and data for each target.
@@ -249,7 +249,7 @@ def multi_target_shap_summary_plot(
         save_dir (str | Path): Directory to save SHAP artifacts.
         device (torch.device): The torch device for SHAP calculations.
         explainer_type (Literal['deep', 'kernel']): The explainer to use.
-            - 'deep': (Default) Uses shap.DeepExplainer. Fast and efficient.
+            - 'deep': Uses shap.DeepExplainer. Fast and efficient.
             - 'kernel': Uses shap.KernelExplainer. Model-agnostic but slow and memory-intensive.
     """
     _LOGGER.info(f"--- Multi-Target SHAP Value Explanation (Using: {explainer_type.upper()}Explainer) ---")
@@ -260,7 +260,7 @@ def multi_target_shap_summary_plot(
     instances_to_explain_np = None
 
     if explainer_type == 'deep':
-        # --- 1. Use DeepExplainer (Preferred) ---
+        # --- 1. Use DeepExplainer ---
         
         # Ensure data is torch.Tensor
         if isinstance(background_data, np.ndarray):
@@ -285,10 +285,9 @@ def multi_target_shap_summary_plot(
         instances_to_explain_np = instances_to_explain.cpu().numpy()
 
     elif explainer_type == 'kernel':
-        # --- 2. Use KernelExplainer (Slow Fallback) ---
+        # --- 2. Use KernelExplainer  ---
         _LOGGER.warning(
-            "Using KernelExplainer. This is memory-intensive and slow. "
-            "Consider reducing 'n_samples' if the process terminates."
+            "KernelExplainer is memory-intensive and slow. Consider reducing the number of instances to explain if the process terminates unexpectedly."
         )
         
         # Convert all data to numpy

{dragon_ml_toolbox-13.3.2 → dragon_ml_toolbox-13.5.0}/ml_tools/ML_trainer.py

@@ -9,7 +9,7 @@ from .ML_callbacks import Callback, History, TqdmProgressBar, ModelCheckpoint
 from .ML_evaluation import classification_metrics, regression_metrics, plot_losses, shap_summary_plot, plot_attention_importance
 from .ML_evaluation_multi import multi_target_regression_metrics, multi_label_classification_metrics, multi_target_shap_summary_plot
 from ._script_info import _script_info
-from .keys import PyTorchLogKeys, PyTorchCheckpointKeys
+from .keys import PyTorchLogKeys, PyTorchCheckpointKeys, DatasetKeys
 from ._logger import _LOGGER
 from .path_manager import make_fullpath
 
@@ -408,7 +408,7 @@ class MLTrainer:
                 n_samples: int = 300,
                 feature_names: Optional[List[str]] = None,
                 target_names: Optional[List[str]] = None,
-                explainer_type: Literal['deep', 'kernel'] = 'deep'):
+                explainer_type: Literal['deep', 'kernel'] = 'kernel'):
         """
         Explains model predictions using SHAP and saves all artifacts.
 
@@ -422,11 +422,11 @@ class MLTrainer:
             explain_dataset (Dataset | None): A specific dataset to explain. 
                                                  If None, the trainer's test dataset is used.
             n_samples (int): The number of samples to use for both background and explanation.
-            feature_names (list[str] | None): Feature names.
+            feature_names (list[str] | None): Feature names. If None, the names will be extracted from the Dataset and raise an error on failure.
             target_names (list[str] | None): Target names for multi-target tasks.
             save_dir (str | Path): Directory to save all SHAP artifacts.
             explainer_type (Literal['deep', 'kernel']): The explainer to use.
-                - 'deep': (Default) Uses shap.DeepExplainer. Fast and efficient for PyTorch models.
+                - 'deep': Uses shap.DeepExplainer. Fast and efficient for PyTorch models.
                 - 'kernel': Uses shap.KernelExplainer. Model-agnostic but EXTREMELY slow and memory-intensive. Use with a very low 'n_samples'< 100.
         """
         # Internal helper to create a dataloader and get a random sample
@@ -474,10 +474,10 @@ class MLTrainer:
         # attempt to get feature names
         if feature_names is None:
             # _LOGGER.info("`feature_names` not provided. Attempting to extract from dataset...")
-            if hasattr(target_dataset, "feature_names"):
+            if hasattr(target_dataset, DatasetKeys.FEATURE_NAMES):
                 feature_names = target_dataset.feature_names # type: ignore
             else:
-                _LOGGER.error("Could not extract `feature_names` from the dataset. It must be provided if the dataset object does not have a `feature_names` attribute.")
+                _LOGGER.error(f"Could not extract `feature_names` from the dataset. It must be provided if the dataset object does not have a '{DatasetKeys.FEATURE_NAMES}' attribute.")
                 raise ValueError()
             
         # move model to device
@@ -498,7 +498,7 @@ class MLTrainer:
             # try to get target names
             if target_names is None:
                 target_names = []
-                if hasattr(target_dataset, 'target_names'):
+                if hasattr(target_dataset, DatasetKeys.TARGET_NAMES):
                     target_names = target_dataset.target_names # type: ignore
                 else:
                     # Infer number of targets from the model's output layer
@@ -549,7 +549,7 @@ class MLTrainer:
                 yield attention_weights
     
     def explain_attention(self, save_dir: Union[str, Path], 
-                          feature_names: Optional[List[str]], 
+                          feature_names: Optional[List[str]] = None, 
                           explain_dataset: Optional[Dataset] = None,
                           plot_n_features: int = 10):
         """
@@ -559,7 +559,7 @@ class MLTrainer:
 
         Args:
             save_dir (str | Path): Directory to save the plot and summary data.
-            feature_names (List[str] | None): Names for the features for plot labeling. If not given, generic names will be used.
+            feature_names (List[str] | None): Names for the features for plot labeling. If None, the names will be extracted from the Dataset and raise an error on failure.
             explain_dataset (Dataset, optional): A specific dataset to explain. If None, the trainer's test dataset is used.
             plot_n_features (int): Number of top features to plot.
         """
@@ -580,6 +580,14 @@ class MLTrainer:
             _LOGGER.error("The explanation dataset is empty or invalid. Skipping attention analysis.")
             return
         
+        # Get feature names
+        if feature_names is None:
+            if hasattr(dataset_to_use, DatasetKeys.FEATURE_NAMES):
+                feature_names = dataset_to_use.feature_names # type: ignore
+            else:
+                _LOGGER.error(f"Could not extract `feature_names` from the dataset for attention plot. It must be provided if the dataset object does not have a '{DatasetKeys.FEATURE_NAMES}' attribute.")
+                raise ValueError()
+        
         explain_loader = DataLoader(
             dataset=dataset_to_use, batch_size=32, shuffle=False,
             num_workers=0 if self.device.type == 'mps' else self.dataloader_workers,

{dragon_ml_toolbox-13.3.2 → dragon_ml_toolbox-13.5.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "dragon-ml-toolbox"
-version = "13.3.2"
+version = "13.5.0"
 description = "A collection of tools for data science and machine learning projects."
 authors = [
     { name = "Karl L. Loza Vidaurre", email = "luigiloza@gmail.com" }