alchemist-nrel 0.3.1__py3-none-any.whl → 0.3.2__py3-none-any.whl

alchemist_core/__init__.py

@@ -27,10 +27,10 @@ Example:
     >>> # Get next experiment suggestion
     >>> next_point = session.suggest_next(acq_func="ei")
 
-Version: 0.3.0-beta.1
+Version: 0.3.2
 """
 
-__version__ = "0.3.0b1"
+__version__ = "0.3.2"
 __author__ = "Caleb Coatney"
 __email__ = "caleb.coatney@nrel.gov"
 

alchemist_core/acquisition/botorch_acquisition.py

@@ -312,6 +312,10 @@ class BoTorchAcquisition(BaseAcquisition):
                         options=options,
                     )
                     
+                    # Log the acquisition value found
+                    acq_val = batch_acq_values.item() if batch_acq_values.numel() == 1 else batch_acq_values.max().item()
+                    logger.info(f"Optimization found acquisition value: {acq_val:.4f}")
+                    
                     # Get the best candidate(s)
                     best_candidates = batch_candidates.detach().cpu()
                     
@@ -533,7 +537,14 @@ class BoTorchAcquisition(BaseAcquisition):
         return self
 
     def find_optimum(self, model=None, maximize=None, random_state=None):
-        """Find the point where the model predicts the optimal value."""
+        """
+        Find the point where the model predicts the optimal value.
+        
+        This uses the same approach as regret plot predictions: generate a grid
+        in the original variable space, predict using the model's standard pipeline,
+        and find the argmax/argmin. This ensures categorical variables are handled
+        correctly through proper encoding/decoding.
+        """
         if model is not None:
             self.model = model
             
@@ -543,135 +554,81 @@ class BoTorchAcquisition(BaseAcquisition):
         if random_state is not None:
             self.random_state = random_state
     
-        # Get bounds from the search space
-        bounds_tensor = self._get_bounds_from_search_space()
+        # Generate prediction grid in ORIGINAL variable space (not encoded)
+        # This handles categorical variables correctly
+        n_grid_points = 10000  # Target number of grid points
+        grid = self._generate_prediction_grid(n_grid_points)
+        
+        # Use model's predict method which handles encoding internally
+        # This is the same pipeline used by regret plot (correct approach)
+        means, stds = self.model.predict(grid, return_std=True)
+        
+        # Find argmax or argmin
+        if self.maximize:
+            best_idx = np.argmax(means)
+        else:
+            best_idx = np.argmin(means)
         
-        # Identify categorical and integer variables
-        categorical_variables = []
-        integer_variables = []
-        if hasattr(self.search_space_obj, 'get_categorical_variables'):
-            categorical_variables = self.search_space_obj.get_categorical_variables()
-        if hasattr(self.search_space_obj, 'get_integer_variables'):
-            integer_variables = self.search_space_obj.get_integer_variables()
+        # Extract the optimal point (already in original variable space)
+        opt_point_df = grid.iloc[[best_idx]].reset_index(drop=True)
+        
+        return {
+            'x_opt': opt_point_df,
+            'value': float(means[best_idx]),
+            'std': float(stds[best_idx])
+        }
     
-        # Prepare for optimization
-        torch.manual_seed(self.random_state)
+    def _generate_prediction_grid(self, n_grid_points: int) -> pd.DataFrame:
+        """
+        Generate grid of test points across search space for predictions.
         
-        try:
-            # Use a simpler randomized search approach instead of optimize_acqf
-            # This avoids the dimension issues in the more complex optimization
-            n_samples = 20000  # Large number of random samples 
-            best_value = float('-inf') if self.maximize else float('inf')
-            best_x = None
-            
-            # Generate random samples within bounds
-            lower_bounds, upper_bounds = bounds_tensor[0], bounds_tensor[1]
-            X_samples = torch.rand(n_samples, len(lower_bounds), dtype=torch.double)
-            X_samples = X_samples * (upper_bounds - lower_bounds) + lower_bounds
-            
-            # Round integer variables to nearest integer
-            if integer_variables:
-                for i, feature_name in enumerate(self.model.feature_names):
-                    if feature_name in integer_variables:
-                        X_samples[:, i] = torch.round(X_samples[:, i])
-            
-            # Evaluate model at all samples
-            self.model.model.eval()
-            with torch.no_grad():
-                posterior = self.model.model.posterior(X_samples)
-                values = posterior.mean.squeeze()
-                
-                # If minimizing, negate values for finding maximum
-                if not self.maximize:
-                    values = -values
-                    
-                # Find the best value
-                best_idx = torch.argmax(values)
-                best_x = X_samples[best_idx]
-                best_value = values[best_idx].item()
-                
-            # Convert to numpy
-            best_candidate = best_x.cpu().numpy().reshape(1, -1)
-        except Exception as e:
-            logger.error(f"Error in random search optimization: {e}")
-            # Fallback to grid search
-            logger.info("Falling back to grid search...")
-            
-            # Create a simple grid search
-            n_points = 10  # Points per dimension
-            grid_points = []
-            
-            # Create grid for each dimension
-            for i, feature_name in enumerate(self.model.feature_names):
-                if feature_name in integer_variables:
-                    # For integer variables, create integer grid
-                    min_val = int(lower_bounds[i])
-                    max_val = int(upper_bounds[i])
-                    if max_val - min_val + 1 <= n_points:
-                        # If range is small, use all integer values
-                        grid_points.append(torch.arange(min_val, max_val + 1, dtype=torch.double))
-                    else:
-                        # If range is large, sample n_points integers
-                        step = max(1, (max_val - min_val) // (n_points - 1))
-                        values = torch.arange(min_val, max_val + 1, step, dtype=torch.double)
-                        grid_points.append(values[:n_points])
+        This creates a grid in the ORIGINAL variable space (with actual category
+        names, not encoded values), which is then properly encoded by the model's
+        predict() method.
+        
+        Args:
+            n_grid_points: Target number of grid points (actual number depends on dimensionality)
+        
+        Returns:
+            DataFrame with columns for each variable in original space
+        """
+        from itertools import product
+        
+        grid_1d = []
+        var_names = []
+        
+        variables = self.search_space_obj.variables
+        n_vars = len(variables)
+        n_per_dim = max(2, int(n_grid_points ** (1/n_vars)))
+        
+        for var in variables:
+            var_names.append(var['name'])
+            
+            if var['type'] == 'real':
+                # Continuous: linspace
+                grid_1d.append(np.linspace(var['min'], var['max'], n_per_dim))
+            elif var['type'] == 'integer':
+                # Integer: range of integers
+                n_integers = var['max'] - var['min'] + 1
+                if n_integers <= n_per_dim:
+                    # Use all integers if range is small
+                    grid_1d.append(np.arange(var['min'], var['max'] + 1))
                 else:
-                    # For continuous variables, use linspace
-                    grid_points.append(torch.linspace(
-                        lower_bounds[i], upper_bounds[i], n_points, dtype=torch.double
-                    ))
-            
-            # Create meshgrid
-            meshgrid = torch.meshgrid(*grid_points, indexing='ij')
-            X_grid = torch.stack([x.reshape(-1) for x in meshgrid], dim=1)
-            
-            # Evaluate model on grid
-            self.model.model.eval()
-            with torch.no_grad():
-                posterior = self.model.model.posterior(X_grid)
-                values = posterior.mean.squeeze()
-                
-                # If minimizing, negate values
-                if not self.maximize:
-                    values = -values
-                    
-                # Find the best value
-                best_idx = torch.argmax(values)
-                best_x = X_grid[best_idx]
-                best_value = values[best_idx].item()
-                
-            # Convert to numpy
-            best_candidate = best_x.cpu().numpy().reshape(1, -1)
-            
-        # Convert to dictionary and then to DataFrame
-        feature_names = self.model.original_feature_names
-        result = {}
-        for i, name in enumerate(feature_names):
-            value = best_candidate[0, i]
-            
-            # If this is a categorical variable, convert back to original value
-            if name in categorical_variables:
-                # Find the original categorical value from the encoding
-                encoding = self.model.categorical_encodings.get(name, {})
-                inv_encoding = {v: k for k, v in encoding.items()}
-                if value in inv_encoding:
-                    value = inv_encoding[value]
-                elif int(value) in inv_encoding:
-                    value = inv_encoding[int(value)]
-            # If this is an integer variable, ensure it's an integer
-            elif name in integer_variables:
-                value = int(round(value))
+                    # Sample n_per_dim integers
+                    grid_1d.append(np.linspace(var['min'], var['max'], n_per_dim).astype(int))
+            elif var['type'] == 'categorical':
+                # Categorical: use ACTUAL category values (not encoded)
+                grid_1d.append(var['values'])
         
-            result[name] = value
-            
-        # Convert to DataFrame
-        opt_point_df = pd.DataFrame([result])
+        # Generate test points using Cartesian product
+        X_test_tuples = list(product(*grid_1d))
         
-        # Get predicted value and std at optimum
-        pred_mean, pred_std = self.model.predict_with_std(opt_point_df)
+        # Convert to DataFrame with proper variable names and types
+        grid = pd.DataFrame(X_test_tuples, columns=var_names)
         
-        return {
-            'x_opt': opt_point_df,
-            'value': float(pred_mean[0]),
-            'std': float(pred_std[0])
-        }
+        # Ensure correct dtypes for categorical variables
+        for var in variables:
+            if var['type'] == 'categorical':
+                grid[var['name']] = grid[var['name']].astype(str)
+        
+        return grid

alchemist_core/data/experiment_manager.py

@@ -8,12 +8,20 @@ class ExperimentManager:
     """
     Class for storing and managing experimental data in a consistent way across backends.
     Provides methods for data access, saving/loading, and conversion to formats needed by different backends.
+    
+    Supports both single-objective and multi-objective optimization:
+    - Single-objective: Uses single target column (default: 'Output', but configurable)
+    - Multi-objective: Uses multiple target columns specified in target_columns attribute
+    
+    The target_column parameter allows flexible column naming to support various CSV formats.
     """
-    def __init__(self, search_space=None):
+    def __init__(self, search_space=None, target_columns: Optional[List[str]] = None):
         self.df = pd.DataFrame()  # Raw experimental data
         self.search_space = search_space  # Reference to the search space
         self.filepath = None  # Path to saved experiment file
         self._current_iteration = 0  # Track current iteration for audit log
+        # Support flexible target column naming for both single and multi-objective
+        self.target_columns = target_columns or ['Output']  # Default to 'Output' for backward compatibility
         
     def set_search_space(self, search_space):
         """Set or update the search space reference."""
@@ -35,9 +43,9 @@ class ExperimentManager:
         # Create a copy of the point_dict to avoid modifying the original
         new_point = point_dict.copy()
         
-        # Add output value if provided
+        # Add output value if provided (use first target column for single-objective)
         if output_value is not None:
-            new_point['Output'] = output_value
+            new_point[self.target_columns[0]] = output_value
             
         # Add noise value if provided
         if noise_value is not None:
@@ -107,12 +115,20 @@ class ExperimentManager:
         Returns:
             X: Features DataFrame
             y: Target Series
+            
+        Raises:
+            ValueError: If configured target column is not found in data
         """
-        if 'Output' not in self.df.columns:
-            raise ValueError("DataFrame doesn't contain 'Output' column")
+        target_col = self.target_columns[0]  # Use first target column for single-objective
         
-        # Drop metadata columns (Output, Noise, Iteration, Reason)
-        metadata_cols = ['Output']
+        if target_col not in self.df.columns:
+            raise ValueError(
+                f"DataFrame doesn't contain target column '{target_col}'. "
+                f"Available columns: {list(self.df.columns)}"
+            )
+        
+        # Drop metadata columns (target, Noise, Iteration, Reason)
+        metadata_cols = self.target_columns.copy()
         if 'Noise' in self.df.columns:
             metadata_cols.append('Noise')
         if 'Iteration' in self.df.columns:
@@ -121,7 +137,7 @@ class ExperimentManager:
             metadata_cols.append('Reason')
         
         X = self.df.drop(columns=metadata_cols)
-        y = self.df['Output']
+        y = self.df[target_col]
         return X, y
     
     def get_features_target_and_noise(self) -> Tuple[pd.DataFrame, pd.Series, Optional[pd.Series]]:
@@ -132,12 +148,20 @@ class ExperimentManager:
             X: Features DataFrame
             y: Target Series
             noise: Noise Series if available, otherwise None
+            
+        Raises:
+            ValueError: If configured target column is not found in data
         """
-        if 'Output' not in self.df.columns:
-            raise ValueError("DataFrame doesn't contain 'Output' column")
+        target_col = self.target_columns[0]  # Use first target column for single-objective
+        
+        if target_col not in self.df.columns:
+            raise ValueError(
+                f"DataFrame doesn't contain target column '{target_col}'. "
+                f"Available columns: {list(self.df.columns)}"
+            )
         
         # Drop metadata columns
-        metadata_cols = ['Output']
+        metadata_cols = self.target_columns.copy()
         if 'Noise' in self.df.columns:
             metadata_cols.append('Noise')
         if 'Iteration' in self.df.columns:
@@ -146,7 +170,7 @@ class ExperimentManager:
             metadata_cols.append('Reason')
         
         X = self.df.drop(columns=metadata_cols)
-        y = self.df['Output']
+        y = self.df[target_col]
         noise = self.df['Noise'] if 'Noise' in self.df.columns else None
         return X, y, noise
     
@@ -224,3 +248,148 @@ class ExperimentManager:
     
     def __len__(self):
         return len(self.df)
+    
+    def get_pareto_frontier(self, directions: Optional[List[str]] = None) -> pd.DataFrame:
+        """
+        Compute Pareto-optimal solutions from experiments with multiple objectives.
+        
+        Uses BoTorch's fast non-dominated sorting algorithm to identify Pareto-optimal
+        points. Works with both single-objective (returns all data) and multi-objective
+        experiments.
+        
+        Args:
+            directions: List of 'maximize' or 'minimize' for each target column.
+                       If None, assumes all objectives are maximized.
+                       Length must match number of target columns.
+        
+        Returns:
+            DataFrame containing only Pareto-optimal experiments with all columns.
+            
+        Raises:
+            ValueError: If directions length doesn't match target columns.
+            ValueError: If target columns contain missing data.
+            
+        Example:
+            >>> # For 2 objectives: maximize yield, minimize cost
+            >>> pareto_df = exp_mgr.get_pareto_frontier(['maximize', 'minimize'])
+        """
+        import torch
+        from botorch.utils.multi_objective.pareto import is_non_dominated
+        
+        if len(self.df) == 0:
+            return pd.DataFrame()
+        
+        # Validate target columns exist
+        missing_cols = [col for col in self.target_columns if col not in self.df.columns]
+        if missing_cols:
+            raise ValueError(f"Target columns {missing_cols} not found in experiment data")
+        
+        # Extract objective values
+        Y = self.df[self.target_columns].values
+        
+        # Check for missing values
+        if pd.isna(Y).any():
+            raise ValueError("Target columns contain missing values (NaN). Cannot compute Pareto frontier.")
+        
+        # Single objective case: return all data
+        if len(self.target_columns) == 1:
+            return self.df.copy()
+        
+        # Set default directions if not provided
+        if directions is None:
+            directions = ['maximize'] * len(self.target_columns)
+        
+        # Validate directions
+        if len(directions) != len(self.target_columns):
+            raise ValueError(
+                f"Number of directions ({len(directions)}) must match number of "
+                f"target columns ({len(self.target_columns)})"
+            )
+        
+        # Convert objectives to maximization form (BoTorch assumes maximization)
+        Y_torch = torch.tensor(Y, dtype=torch.double)
+        for i, direction in enumerate(directions):
+            if direction.lower() == 'minimize':
+                Y_torch[:, i] = -Y_torch[:, i]
+        
+        # Compute non-dominated mask
+        nd_mask = is_non_dominated(Y_torch, maximize=True, deduplicate=True)
+        
+        # Return Pareto-optimal experiments
+        return self.df[nd_mask.numpy()].copy()
+    
+    def compute_hypervolume(self, ref_point: Union[List[float], np.ndarray], 
+                           directions: Optional[List[str]] = None) -> float:
+        """
+        Compute hypervolume indicator for multi-objective experiments.
+        
+        The hypervolume measures the volume of objective space dominated by the
+        Pareto frontier relative to a reference point. Larger values indicate
+        better overall performance.
+        
+        Args:
+            ref_point: Reference point (worst acceptable values) for each objective.
+                      Must have same length as target_columns.
+                      For maximization: should be below minimum observed values.
+                      For minimization: should be above maximum observed values.
+            directions: List of 'maximize' or 'minimize' for each target column.
+                       If None, assumes all objectives are maximized.
+        
+        Returns:
+            Hypervolume value (float). Zero if no Pareto-optimal points exist.
+            
+        Raises:
+            ValueError: If ref_point length doesn't match target columns.
+            ValueError: If target columns contain missing data.
+            
+        Example:
+            >>> # For 2 objectives (maximize yield, minimize cost)
+            >>> # ref_point = [min_acceptable_yield, max_acceptable_cost]
+            >>> hv = exp_mgr.compute_hypervolume([50.0, 100.0], ['maximize', 'minimize'])
+        """
+        import torch
+        from botorch.utils.multi_objective.hypervolume import Hypervolume
+        
+        if len(self.df) == 0:
+            return 0.0
+        
+        # Single objective case: not meaningful
+        if len(self.target_columns) == 1:
+            raise ValueError(
+                "Hypervolume is only defined for multi-objective problems. "
+                "For single-objective, use best observed value instead."
+            )
+        
+        # Validate ref_point
+        ref_point = np.array(ref_point)
+        if len(ref_point) != len(self.target_columns):
+            raise ValueError(
+                f"Reference point length ({len(ref_point)}) must match number of "
+                f"target columns ({len(self.target_columns)})"
+            )
+        
+        # Get Pareto frontier
+        pareto_df = self.get_pareto_frontier(directions)
+        if len(pareto_df) == 0:
+            return 0.0
+        
+        # Set default directions if not provided
+        if directions is None:
+            directions = ['maximize'] * len(self.target_columns)
+        
+        # Extract Pareto objectives and convert to torch tensors
+        Y_pareto = pareto_df[self.target_columns].values
+        Y_torch = torch.tensor(Y_pareto, dtype=torch.double)
+        ref_torch = torch.tensor(ref_point, dtype=torch.double)
+        
+        # Convert to maximization form (BoTorch assumes maximization)
+        for i, direction in enumerate(directions):
+            if direction.lower() == 'minimize':
+                Y_torch[:, i] = -Y_torch[:, i]
+                ref_torch[i] = -ref_torch[i]
+        
+        # Compute hypervolume
+        hv_calculator = Hypervolume(ref_point=ref_torch)
+        hv = hv_calculator.compute(Y_torch)
+        
+        return float(hv)