sciml 0.0.8__tar.gz → 0.0.9__tar.gz

{sciml-0.0.8 → sciml-0.0.9}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2021 Zhu
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2021 Zhu
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{sciml-0.0.8 → sciml-0.0.9}/PKG-INFO

@@ -1,13 +1,13 @@
-Metadata-Version: 2.1
-Name: sciml
-Version: 0.0.8
-Summary: draw and basic calculations/conversions
-Home-page: https://github.com/soonyenju/sciml
-Author: Songyan Zhu
-Author-email: zhusy93@gmail.com
-License: MIT Licence
-Keywords: Scientific machine learning wrappers
-Platform: any
-License-File: LICENSE
-
-coming soon
+Metadata-Version: 2.1
+Name: sciml
+Version: 0.0.9
+Summary: draw and basic calculations/conversions
+Home-page: https://github.com/soonyenju/sciml
+Author: Songyan Zhu
+Author-email: zhusy93@gmail.com
+License: MIT Licence
+Keywords: Scientific machine learning wrappers
+Platform: any
+License-File: LICENSE
+
+coming soon

{sciml-0.0.8 → sciml-0.0.9}/README.md

@@ -1,7 +1,7 @@
-# SCIentific Machine Learning (sciml)
- 
-Author: Dr. Songyan Zhu University of Southampton
-
-Contact: Songyan.Zhu@ed.soton.uk
-
-Website: https://sites.google.com/view/uflux
+# SCIentific Machine Learning (sciml)
+ 
+Author: Dr. Songyan Zhu University of Southampton
+
+Contact: Songyan.Zhu@ed.soton.uk
+
+Website: https://sites.google.com/view/uflux

sciml-0.0.9/sciml/__init__.py

@@ -0,0 +1,2 @@
+# coding: utf-8
+__all__ = ["utils", "pipelines", "models"]

{sciml-0.0.8 → sciml-0.0.9}/sciml/models.py

@@ -1,269 +1,277 @@
-import numpy as np
-import copy
-import itertools
-import warnings
-from xgboost import XGBRegressor
-from sklearn.metrics import mean_squared_error
-from sklearn.model_selection import train_test_split
-
-class SmartForest:
-    """
-    SmartForest: A deep, intelligent decision forest model for complex sequential and tabular data.
-
-    SmartForest blends ideas from deep forests (cascade forest structures), LSTM-style forget gates,
-    and ensemble learning using XGBoost. It is especially suited for time series or structured tabular data 
-    where layer-wise feature expansion and memory-inspired filtering can enhance performance.
-
-    Key Features:
-    -------------
-    - Deep cascade of XGBoost regressors
-    - Optional Multi-Grained Scanning (MGS) for local feature extraction
-    - Forget-gate-inspired mechanism to regulate information flow across layers
-    - Early stopping to prevent overfitting
-    - Full retention of best-performing model (lowest validation RMSE)
-
-    Parameters:
-    -----------
-    n_estimators_per_layer : int
-        Number of XGBoost regressors per layer.
-    
-    max_layers : int
-        Maximum number of layers (depth) in the model.
-
-    early_stopping_rounds : int
-        Number of layers with no improvement before early stopping is triggered.
-
-    param_grid : dict
-        Grid of XGBoost hyperparameters to search over.
-
-    use_gpu : bool
-        If True, use GPU-accelerated training (CUDA required).
-
-    gpu_id : int
-        ID of GPU to use (if use_gpu=True).
-
-    window_sizes : list of int
-        Enables Multi-Grained Scanning if non-empty, with specified sliding window sizes.
-
-    forget_factor : float in [0, 1]
-        Simulates LSTM-style forget gate; higher values forget more past information.
-
-    verbose : int
-        Verbosity level (0 = silent, 1 = progress updates).
-
-    Methods:
-    --------
-    fit(X, y, X_val=None, y_val=None):
-        Train the SmartForest model layer by layer, using optional validation for early stopping.
-
-    predict(X):
-        Make predictions on new data using the trained cascade structure.
-
-    get_best_model():
-        Returns a copy of the best model and the corresponding RMSE from validation.
-
-    Example:
-    --------
-    >>> model = SmartForest(n_estimators_per_layer=5, max_layers=10, window_sizes=[2, 3], forget_factor=0.2)
-    >>> model.fit(X_train, y_train, X_val, y_val)
-    >>> y_pred = model.predict(X_val)
-    >>> best_model, best_rmse = model.get_best_model()
-    """
-    def __init__(self, n_estimators_per_layer = 5, max_layers = 10, early_stopping_rounds = 3, param_grid = None,
-                 use_gpu = False, gpu_id = 0, window_sizes = [], forget_factor = 0, verbose = 1):
-        self.n_estimators_per_layer = n_estimators_per_layer
-        self.max_layers = max_layers
-        self.early_stopping_rounds = early_stopping_rounds
-        self.param_grid = param_grid or {
-            "objective": ["reg:squarederror"],
-            "random_state": [42],
-            'seed': [0],
-            'n_estimators': [100],
-            'max_depth': [6],
-            'min_child_weight': [4],
-            'subsample': [0.8],
-            'colsample_bytree': [0.8],
-            'gamma': [0],
-            'reg_alpha': [0],
-            'reg_lambda': [1],
-            'learning_rate': [0.05],
-        }
-        self.use_gpu = use_gpu
-        self.gpu_id = gpu_id
-        self.window_sizes = window_sizes
-        self.forget_factor = forget_factor
-        self.layers = []
-        self.best_model = None
-        self.best_rmse = float("inf")
-        self.verbose = verbose
-
-    def _get_param_combinations(self):
-        keys, values = zip(*self.param_grid.items())
-        return [dict(zip(keys, v)) for v in itertools.product(*values)]
-
-    def _multi_grained_scanning(self, X, y):
-        new_features = []
-        for window_size in self.window_sizes:
-            if X.shape[1] < window_size:
-                continue
-            for start in range(X.shape[1] - window_size + 1):
-                window = X[:, start:start + window_size]
-                if y is None:
-                    new_features.append(window)
-                    continue
-
-                param_combos = self._get_param_combinations()
-                for params in param_combos:
-                    if self.use_gpu:
-                        params['tree_method'] = 'hist'
-                        params['device'] = 'cuda'
-                    model = XGBRegressor(**params)
-                    model.fit(window, y)
-                    preds = model.predict(window).reshape(-1, 1)
-                    new_features.append(preds)
-        return np.hstack(new_features) if new_features else X
-
-    def _apply_forget_gate(self, X, layer_index):
-        forget_weights = np.random.rand(X.shape[1]) * self.forget_factor
-        return X * (1 - forget_weights)
-
-    def _fit_layer(self, X, y, X_val=None, y_val=None, layer_index=0):
-        layer = []
-        layer_outputs = []
-        param_combos = self._get_param_combinations()
-        X = self._apply_forget_gate(X, layer_index)
-
-        for i in range(self.n_estimators_per_layer):
-            best_rmse = float('inf')
-            best_model = None
-
-            for params in param_combos:
-                if self.use_gpu:
-                    params['tree_method'] = 'hist'
-                    params['device'] = 'cuda'
-
-                model = XGBRegressor(**params)
-                model.fit(X, y)
-
-                if X_val is not None:
-                    preds_val = model.predict(X_val)
-                    rmse = np.sqrt(mean_squared_error(y_val, preds_val))
-                    if rmse < best_rmse:
-                        best_rmse = rmse
-                        best_model = model
-                else:
-                    best_model = model
-
-            preds = best_model.predict(X).reshape(-1, 1)
-            layer.append(best_model)
-            layer_outputs.append(preds)
-
-        output = np.hstack(layer_outputs)
-        return layer, output
-
-    def fit(self, X, y, X_val=None, y_val=None):
-        X_current = self._multi_grained_scanning(X, y)
-        X_val_current = self._multi_grained_scanning(X_val, y_val) if X_val is not None else None
-        no_improve_rounds = 0
-
-        for layer_index in range(self.max_layers):
-            if self.verbose: print(f"Training Layer {layer_index + 1}")
-            layer, output = self._fit_layer(X_current, y, X_val_current, y_val, layer_index)
-            self.layers.append(layer)
-            X_current = np.hstack([X_current, output])
-
-            if X_val is not None:
-                val_outputs = []
-                for reg in layer:
-                    n_features = reg.n_features_in_
-                    preds = reg.predict(X_val_current[:, :n_features]).reshape(-1, 1)
-                    val_outputs.append(preds)
-                val_output = np.hstack(val_outputs)
-                X_val_current = np.hstack([X_val_current, val_output])
-
-                y_pred = self.predict(X_val)
-                rmse = np.sqrt(mean_squared_error(y_val, y_pred))
-                if self.verbose: print(f"Validation RMSE: {rmse:.4f}")
-
-                if rmse < self.best_rmse:
-                    self.best_rmse = rmse
-                    self.best_model = copy.deepcopy(self.layers)
-                    no_improve_rounds = 0
-                    if self.verbose: print(f"✅ New best RMSE: {self.best_rmse:.4f}")
-                else:
-                    no_improve_rounds += 1
-                    if no_improve_rounds >= self.early_stopping_rounds:
-                        if self.verbose: print("Early stopping triggered.")
-                        break
-
-    def predict(self, X):
-        X_current = self._multi_grained_scanning(X, None)
-        X_current = self._apply_forget_gate(X_current, layer_index=-1)
-
-        for layer in self.layers:
-            layer_outputs = []
-            for reg in layer:
-                n_features = reg.n_features_in_
-                preds = reg.predict(X_current[:, :n_features]).reshape(-1, 1)
-                layer_outputs.append(preds)
-            output = np.hstack(layer_outputs)
-            X_current = np.hstack([X_current, output])
-
-        final_outputs = []
-        for reg in self.layers[-1]:
-            n_features = reg.n_features_in_
-            final_outputs.append(reg.predict(X_current[:, :n_features]).reshape(-1, 1))
-        return np.mean(np.hstack(final_outputs), axis=1)
-
-    def get_best_model(self):
-        return self.best_model, self.best_rmse
-
-"""
-# ============================== Test Example ==============================
-from sklearn.datasets import load_diabetes
-
-warnings.simplefilter('ignore')
-
-X, y = load_diabetes(return_X_y=True)
-X_train, X_val, y_train, y_val = train_test_split(X, y, test_size=0.3, random_state=42)
-
-# Hyperparameter grid
-param_grid = {
-    "objective": ["reg:squarederror"],
-    "random_state": [42],
-    'seed': [0],
-    'n_estimators': [100],
-    'max_depth': [6],
-    'min_child_weight': [4],
-    'subsample': [0.8],
-    'colsample_bytree': [0.8],
-    'gamma': [0],
-    'reg_alpha': [0],
-    'reg_lambda': [1],
-    'learning_rate': [0.05],
-}
-
-# Create the model with Multi-Grained Scanning enabled (with window sizes 2 and 3)
-df_reg = SmartForest(
-    n_estimators_per_layer = 5,
-    max_layers = 10,
-    early_stopping_rounds = 5,
-    param_grid = param_grid,
-    use_gpu = False,
-    gpu_id = 0,
-    window_sizes = [],  # Enables MGS if e.g., [2, 3], else empty disables MGS.
-    forget_factor = 0.,  # Set forget factor to simulate forget gate behavior
-    verbose = 1
-)
-
-df_reg.fit(X_train, y_train, X_val, y_val)
-
-# Predict on validation set and evaluate
-y_pred = df_reg.predict(X_val)
-rmse = np.sqrt(mean_squared_error(y_val, y_pred))
-print("\nFinal RMSE:", rmse)
-
-# Output best model and RMSE
-best_model, best_rmse = df_reg.get_best_model()
-print("\nBest validation RMSE:", best_rmse)
+import numpy as np
+import copy
+import itertools
+import warnings
+from xgboost import XGBRegressor
+from sklearn.metrics import mean_squared_error
+from sklearn.model_selection import train_test_split
+
+class SmartForest:
+    """
+    SmartForest: A deep, intelligent decision forest model for complex sequential and tabular data.
+
+    SmartForest blends ideas from deep forests (cascade forest structures), LSTM-style forget gates,
+    and ensemble learning using XGBoost. It is especially suited for time series or structured tabular data 
+    where layer-wise feature expansion and memory-inspired filtering can enhance performance.
+
+    Key Features:
+    -------------
+    - Deep cascade of XGBoost regressors
+    - Optional Multi-Grained Scanning (MGS) for local feature extraction
+    - Forget-gate-inspired mechanism to regulate information flow across layers
+    - Early stopping to prevent overfitting
+    - Full retention of best-performing model (lowest validation RMSE)
+
+    Parameters:
+    -----------
+    n_estimators_per_layer : int
+        Number of XGBoost regressors per layer.
+    
+    max_layers : int
+        Maximum number of layers (depth) in the model.
+
+    early_stopping_rounds : int
+        Number of layers with no improvement before early stopping is triggered.
+
+    param_grid : dict
+        Grid of XGBoost hyperparameters to search over.
+
+    use_gpu : bool
+        If True, use GPU-accelerated training (CUDA required).
+
+    gpu_id : int
+        ID of GPU to use (if use_gpu=True).
+
+    window_sizes : list of int
+        Enables Multi-Grained Scanning if non-empty, with specified sliding window sizes.
+
+    forget_factor : float in [0, 1]
+        Simulates LSTM-style forget gate; higher values forget more past information.
+
+    verbose : int
+        Verbosity level (0 = silent, 1 = progress updates).
+
+    Methods:
+    --------
+    fit(X, y, X_val=None, y_val=None):
+        Train the SmartForest model layer by layer, using optional validation for early stopping.
+
+    predict(X):
+        Make predictions on new data using the trained cascade structure.
+
+    get_best_model():
+        Returns a copy of the best model and the corresponding RMSE from validation.
+
+    Example:
+    --------
+    >>> model = SmartForest(n_estimators_per_layer=5, max_layers=10, window_sizes=[2, 3], forget_factor=0.2)
+    >>> model.fit(X_train, y_train, X_val, y_val)
+    >>> y_pred = model.predict(X_val)
+    >>> best_model, best_rmse = model.get_best_model()
+    """
+    def __init__(self, n_estimators_per_layer = 5, max_layers = 10, early_stopping_rounds = 3, param_grid = None,
+                 use_gpu = False, gpu_id = 0, window_sizes = [], forget_factor = 0, verbose = 1):
+        self.n_estimators_per_layer = n_estimators_per_layer
+        self.max_layers = max_layers
+        self.early_stopping_rounds = early_stopping_rounds
+        self.param_grid = param_grid or {
+            "objective": ["reg:squarederror"],
+            "random_state": [42],
+            'seed': [0],
+            'n_estimators': [100],
+            'max_depth': [6],
+            'min_child_weight': [4],
+            'subsample': [0.8],
+            'colsample_bytree': [0.8],
+            'gamma': [0],
+            'reg_alpha': [0],
+            'reg_lambda': [1],
+            'learning_rate': [0.05],
+        }
+        self.use_gpu = use_gpu
+        self.gpu_id = gpu_id
+        self.window_sizes = window_sizes
+        self.forget_factor = forget_factor
+        self.layers = []
+        self.best_model = None
+        self.best_rmse = float("inf")
+        self.verbose = verbose
+
+    def _get_param_combinations(self):
+        keys, values = zip(*self.param_grid.items())
+        return [dict(zip(keys, v)) for v in itertools.product(*values)]
+
+    def _multi_grained_scanning(self, X, y):
+        new_features = []
+        for window_size in self.window_sizes:
+            if X.shape[1] < window_size:
+                continue
+            for start in range(X.shape[1] - window_size + 1):
+                window = X[:, start:start + window_size]
+                if y is None:
+                    new_features.append(window)
+                    continue
+
+                param_combos = self._get_param_combinations()
+                for params in param_combos:
+                    if self.use_gpu:
+                        params['tree_method'] = 'hist'
+                        params['device'] = 'cuda'
+                    model = XGBRegressor(**params)
+                    model.fit(window, y)
+                    preds = model.predict(window).reshape(-1, 1)
+                    new_features.append(preds)
+        return np.hstack(new_features) if new_features else X
+
+    def _apply_forget_gate(self, X, layer_index):
+        forget_weights = np.random.rand(X.shape[1]) * self.forget_factor
+        return X * (1 - forget_weights)
+
+    def _fit_layer(self, X, y, X_val=None, y_val=None, layer_index=0):
+        layer = []
+        layer_outputs = []
+        param_combos = self._get_param_combinations()
+        X = self._apply_forget_gate(X, layer_index)
+
+        for i in range(self.n_estimators_per_layer):
+            best_rmse = float('inf')
+            best_model = None
+
+            for params in param_combos:
+                if self.use_gpu:
+                    params['tree_method'] = 'hist'
+                    params['device'] = 'cuda'
+
+                params = params.copy()  # Prevent modification from affecting the next loop iteration
+                params['random_state'] = i  # Use a different random seed for each model to enhance diversity
+
+                model = XGBRegressor(**params)
+                model.fit(X, y)
+
+                if X_val is not None:
+                    preds_val = model.predict(X_val)
+                    rmse = np.sqrt(mean_squared_error(y_val, preds_val))
+                    if rmse < best_rmse:
+                        best_rmse = rmse
+                        best_model = model
+                else:
+                    best_model = model
+
+            preds = best_model.predict(X).reshape(-1, 1)
+            layer.append(best_model)
+            layer_outputs.append(preds)
+
+        output = np.hstack(layer_outputs)
+        return layer, output
+
+    def fit(self, X, y, X_val=None, y_val=None):
+        X_current = self._multi_grained_scanning(X, y)
+        X_val_current = self._multi_grained_scanning(X_val, y_val) if X_val is not None else None
+        no_improve_rounds = 0
+
+        for layer_index in range(self.max_layers):
+            if self.verbose: print(f"Training Layer {layer_index + 1}")
+            layer, output = self._fit_layer(X_current, y, X_val_current, y_val, layer_index)
+            self.layers.append(layer)
+            X_current = np.hstack([X_current, output])
+
+            if X_val is not None:
+                val_outputs = []
+                for reg in layer:
+                    n_features = reg.n_features_in_
+                    preds = reg.predict(X_val_current[:, :n_features]).reshape(-1, 1)
+                    val_outputs.append(preds)
+                val_output = np.hstack(val_outputs)
+                X_val_current = np.hstack([X_val_current, val_output])
+
+                y_pred = self.predict(X_val)
+                rmse = np.sqrt(mean_squared_error(y_val, y_pred))
+                if self.verbose: print(f"Validation RMSE: {rmse:.4f}")
+
+                if rmse < self.best_rmse:
+                    self.best_rmse = rmse
+                    self.best_model = copy.deepcopy(self.layers)
+                    no_improve_rounds = 0
+                    if self.verbose: print(f"✅ New best RMSE: {self.best_rmse:.4f}")
+                else:
+                    no_improve_rounds += 1
+                    if no_improve_rounds >= self.early_stopping_rounds:
+                        if self.verbose: print("Early stopping triggered.")
+                        break
+
+    def predict(self, X):
+        X_current = self._multi_grained_scanning(X, None)
+        X_current = self._apply_forget_gate(X_current, layer_index=-1)
+
+        for layer in self.layers:
+            layer_outputs = []
+            for reg in layer:
+                n_features = reg.n_features_in_
+                preds = reg.predict(X_current[:, :n_features]).reshape(-1, 1)
+                layer_outputs.append(preds)
+            output = np.hstack(layer_outputs)
+            X_current = np.hstack([X_current, output])
+
+        final_outputs = []
+        for reg in self.layers[-1]:
+            n_features = reg.n_features_in_
+            final_outputs.append(reg.predict(X_current[:, :n_features]).reshape(-1, 1))
+        return np.mean(np.hstack(final_outputs), axis=1)
+
+    def get_best_model(self):
+        return self.best_model, self.best_rmse
+
+"""
+# ============================== Test Example ==============================
+from sklearn.datasets import load_diabetes
+from sklearn.datasets import fetch_california_housing
+from sklearn.model_selection import train_test_split
+
+
+
+warnings.simplefilter('ignore')
+
+# X, y = load_diabetes(return_X_y=True) # Using diabetes dataset
+X, y = fetch_california_housing(return_X_y=True) # Using house price dataset
+X_train, X_val, y_train, y_val = train_test_split(X, y, test_size=0.3, random_state=42)
+
+# Hyperparameter grid
+param_grid = {
+    "objective": ["reg:squarederror"],
+    "random_state": [42],
+    'seed': [0],
+    'n_estimators': [100],
+    'max_depth': [6],
+    'min_child_weight': [4],
+    'subsample': [0.8],
+    'colsample_bytree': [0.8],
+    'gamma': [0],
+    'reg_alpha': [0],
+    'reg_lambda': [1],
+    'learning_rate': [0.05],
+}
+
+# Create the model with Multi-Grained Scanning enabled (with window sizes 2 and 3)
+regr = SmartForest(
+    n_estimators_per_layer = 5,
+    max_layers = 10,
+    early_stopping_rounds = 5,
+    param_grid = param_grid,
+    use_gpu = False,
+    gpu_id = 0,
+    window_sizes = [],  # Enables MGS if e.g., [2, 3], else empty disables MGS.
+    forget_factor = 0.,  # Set forget factor to simulate forget gate behavior
+    verbose = 1
+)
+
+regr.fit(X_train, y_train, X_val, y_val)
+
+# Predict on validation set and evaluate
+y_pred = regr.predict(X_val)
+rmse = np.sqrt(mean_squared_error(y_val, y_pred))
+print("\nFinal RMSE:", rmse)
+
+# Output best model and RMSE
+best_model, best_rmse = regr.get_best_model()
+print("\nBest validation RMSE:", best_rmse)
 """