Add new experimentation and parameter

Update README.md

README.md

@@ -1,12 +1,9 @@
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 ![https://img.shields.io/badge/python-3.8%2B-blue](https://img.shields.io/badge/python-3.8%2B-brightgreen)
 
 # benchmark
 
-Benchmarking models
+Benchmarking Python models
 
 ## Experimentation
 

benchmark/Arguments.py

@@ -160,6 +160,15 @@ class Arguments(argparse.ArgumentParser):
                     "help": "Ignore nan results",
                 },
             ],
+            "iwss": [
+                ("--iwss",),
+                {
+                    "default": False,
+                    "action": "store_true",
+                    "required": False,
+                    "help": "Do IWSS with training set and then apply to test set",
+                },
+            ],
             "key": [
                 ("-k", "--key"),
                 {

benchmark/Datasets.py

@@ -32,6 +32,8 @@ class DatasetsArff:
     def get_range_features(X, c_features):
         if c_features.strip() == "all":
             return list(range(X.shape[1]))
+        if c_features.strip() == "none":
+            return []
         return json.loads(c_features)
 
     def load(self, name, class_name):
@@ -129,29 +131,28 @@ class Datasets:
 
     def _init_names(self, dataset_name):
         file_name = os.path.join(self.dataset.folder(), Files.index)
-        default_class = "class"
         self.continuous_features = {}
         with open(file_name) as f:
             sets = f.read().splitlines()
             sets = [x for x in sets if not x.startswith("#")]
-            class_names = [default_class] * len(sets)
+        results = []
-        if "," in sets[0]:
-            result = []
         class_names = []
-            for data in sets:
+        for set_name in sets:
-                name, class_name, features = data.split(",", 2)
+            try:
-                result.append(name)
+                name, class_name, features = set_name.split(";")
+            except ValueError:
+                class_name = "class"
+                features = "all"
+                name = set_name
+            results.append(name)
             class_names.append(class_name)
+            features = features.strip()
             self.continuous_features[name] = features
-            sets = result
-        else:
-            for name in sets:
-                self.continuous_features[name] = None
         # Set as dataset list the dataset passed as argument
         if dataset_name is None:
-            return class_names, sets
+            return class_names, results
         try:
-            class_name = class_names[sets.index(dataset_name)]
+            class_name = class_names[results.index(dataset_name)]
         except ValueError:
             raise ValueError(f"Unknown dataset: {dataset_name}")
         return [class_name], [dataset_name]

benchmark/Experiments.py

@@ -7,12 +7,17 @@ import time
 from datetime import datetime
 from tqdm import tqdm
 import numpy as np
+from mufs import MUFS
 from sklearn.model_selection import (
     StratifiedKFold,
     KFold,
     GridSearchCV,
-    cross_validate,
 )
+from sklearn.svm import LinearSVC
+from sklearn.feature_selection import SelectFromModel
+from sklearn.preprocessing import label_binarize
+from sklearn.base import clone
+from sklearn.metrics import check_scoring, roc_auc_score
 from .Utils import Folders, Files, NO_RESULTS
 from .Datasets import Datasets
 from .Models import Models
@@ -115,6 +120,7 @@ class Experiment:
         ignore_nan=True,
         fit_features=None,
         discretize=None,
+        iwss=False,
         folds=5,
     ):
         env_data = EnvData().load()
@@ -176,6 +182,7 @@ class Experiment:
         self.random_seeds = Randomized.seeds()
         self.results = []
         self.duration = 0
+        self.iwss = iwss
         self._init_experiment()
 
     def get_output_file(self):
@@ -212,48 +219,358 @@ class Experiment:
         res["state_names"] = states
         return res
 
+    # def _n_fold_crossval(self, name, X, y, hyperparameters):
+    #     if self.scores != []:
+    #         raise ValueError("Must init experiment before!")
+
+    #     loop = tqdm(
+    #         self.random_seeds,
+    #         position=1,
+    #         leave=False,
+    #         disable=not self.progress_bar,
+    #     )
+
+    #     for random_state in loop:
+    #         loop.set_description(f"Seed({random_state:4d})")
+    #         random.seed(random_state)
+    #         np.random.seed(random_state)
+
+    #         kfold = self.stratified_class(
+    #             shuffle=True, random_state=random_state, n_splits=self.folds
+    #         )
+
+    #         clf = self._build_classifier(random_state, hyperparameters)
+    #         fit_params = self._build_fit_params(name)
+    #         self.version = Models.get_version(self.model_name, clf)
+
+    #         with warnings.catch_warnings():
+    #             warnings.filterwarnings("ignore")
+
+    #             if self.iwss:
+    #                 # Manual cross-validation with IWSS feature selection
+    #                 fold_scores = []
+    #                 fold_times = []
+    #                 fold_estimators = []
+
+    #                 for train_idx, test_idx in kfold.split(X, y):
+    #                     # Split data
+    #                     X_train, X_test = X[train_idx], X[test_idx]
+    #                     y_train, y_test = y[train_idx], y[test_idx]
+
+    #                     # Apply IWSS feature selection
+    #                     transformer = MUFS()
+    #                     transformer.iwss(X_train, y_train, 0.5)
+    #                     X_train_selected = X_train[
+    #                         :, transformer.get_results()
+    #                     ]
+    #                     X_test_selected = X_test[:, transformer.get_results()]
+    #                     # print("Selected features:", transformer.get_results())
+    #                     # print(
+    #                     #     f"Number of selected features: {X_train_selected.shape[1]}"
+    #                     # )
+
+    #                     # Clone classifier to avoid data leakage between folds
+    #                     clf_fold = clone(clf)
+
+    #                     # Fit the classifier
+    #                     start_time = time.time()
+    #                     clf_fold.fit(X_train_selected, y_train)
+    #                     fit_time = time.time() - start_time
+
+    #                     # Score on test set
+    #                     score_func = get_scorer(
+    #                         self.score_name.replace("-", "_")
+    #                     )
+    #                     # Handle scoring based on the metric type
+    #                     if self.score_name in [
+    #                         "roc_auc",
+    #                         "log_loss",
+    #                         "roc_auc_ovr",
+    #                         "roc_auc_ovo",
+    #                     ]:
+    #                         # These metrics need probabilities
+    #                         if hasattr(clf_fold, "predict_proba"):
+    #                             y_score = clf_fold.predict_proba(
+    #                                 X_test_selected
+    #                             )
+
+    #                             # Handle missing classes in the fold
+    #                             if len(unique_train_classes) < len(
+    #                                 unique_all_classes
+    #                             ):
+    #                                 # Create a full probability matrix with zeros for missing classes
+    #                                 y_score_full = np.zeros(
+    #                                     (len(y_test), len(unique_all_classes))
+    #                                 )
+    #                                 for i, class_label in enumerate(
+    #                                     unique_train_classes
+    #                                 ):
+    #                                     class_idx = np.where(
+    #                                         unique_all_classes == class_label
+    #                                     )[0][0]
+    #                                     y_score_full[:, class_idx] = y_score[
+    #                                         :, i
+    #                                     ]
+    #                                 y_score = y_score_full
+    #                         else:
+    #                             # Fallback to decision_function for SVM-like models
+    #                             y_score = clf_fold.decision_function(
+    #                                 X_test_selected
+    #                             )
+
+    #                         test_score = score_func._score_func(
+    #                             y_test, y_score
+    #                         )
+    #                     else:
+    #                         # For metrics that use predictions (accuracy, f1, etc.)
+    #                         test_score = score_func(
+    #                             clf_fold, X_test_selected, y_test
+    #                         )
+
+    #                     fold_scores.append(test_score)
+    #                     fold_times.append(fit_time)
+    #                     fold_estimators.append(clf_fold)
+
+    #                 # Package results to match cross_validate output format
+    #                 res = {
+    #                     "test_score": np.array(fold_scores),
+    #                     "fit_time": np.array(fold_times),
+    #                     "estimator": fold_estimators,
+    #                 }
+    #             else:
+    #                 # Original cross_validate approach
+    #                 res = cross_validate(
+    #                     clf,
+    #                     X,
+    #                     y,
+    #                     cv=kfold,
+    #                     fit_params=fit_params,
+    #                     return_estimator=True,
+    #                     scoring=self.score_name.replace("-", "_"),
+    #                 )
+
+    #             # Handle NaN values
+    #             if np.isnan(res["test_score"]).any():
+    #                 if not self.ignore_nan:
+    #                     print(res["test_score"])
+    #                     raise ValueError("NaN in results")
+    #                 results = res["test_score"][~np.isnan(res["test_score"])]
+    #             else:
+    #                 results = res["test_score"]
+
+    #             # Store results
+    #             self.scores.extend(results)
+    #             self.times.extend(res["fit_time"])
+
+    #             for result_item in res["estimator"]:
+    #                 nodes_item, leaves_item, depth_item = (
+    #                     Models.get_complexity(self.model_name, result_item)
+    #                 )
+    #                 self.nodes.append(nodes_item)
+    #                 self.leaves.append(leaves_item)
+    #                 self.depths.append(depth_item)
+
+    # from sklearn.base import clone
+    # import numpy as np
+    # import time
+    # import warnings
+    # from tqdm import tqdm
+
     def _n_fold_crossval(self, name, X, y, hyperparameters):
         if self.scores != []:
             raise ValueError("Must init experiment before!")
+
+        # Get all unique classes and check data
+        unique_all_classes = np.sort(np.unique(y))
+        n_classes = len(unique_all_classes)
+
+        # Check if we have enough samples per class for stratified k-fold
+        min_samples_per_class = np.min(np.bincount(y))
+        if min_samples_per_class < self.folds:
+            warnings.warn(
+                f"Class imbalance detected: minimum class has {min_samples_per_class} samples. "
+                f"Consider using fewer folds or handling imbalanced data."
+            )
+
         loop = tqdm(
             self.random_seeds,
             position=1,
             leave=False,
             disable=not self.progress_bar,
         )
+
         for random_state in loop:
             loop.set_description(f"Seed({random_state:4d})")
-            random.seed(random_state)
             np.random.seed(random_state)
+
             kfold = self.stratified_class(
                 shuffle=True, random_state=random_state, n_splits=self.folds
             )
+
             clf = self._build_classifier(random_state, hyperparameters)
             fit_params = self._build_fit_params(name)
             self.version = Models.get_version(self.model_name, clf)
+
+            # Check if the classifier supports probability predictions
+            scorer = check_scoring(clf, scoring="roc_auc_ovr")
+            if not hasattr(clf, "predict_proba") and not hasattr(
+                clf, "decision_function"
+            ):
+                raise ValueError(
+                    f"Classifier {self.model_name} doesn't support probability predictions "
+                    "required for ROC-AUC scoring"
+                )
+
             with warnings.catch_warnings():
                 warnings.filterwarnings("ignore")
-                res = cross_validate(
+
-                    clf,
+                fold_scores = []
-                    X,
+                fold_times = []
-                    y,
+                fold_estimators = []
-                    cv=kfold,
+
-                    fit_params=fit_params,
+                for fold_idx, (train_idx, test_idx) in enumerate(
-                    return_estimator=True,
+                    kfold.split(X, y)
-                    scoring=self.score_name.replace("-", "_"),
+                ):
+                    # Split data
+                    X_train, X_test = X[train_idx], X[test_idx]
+                    y_train, y_test = y[train_idx], y[test_idx]
+
+                    # Check classes in this fold
+                    unique_test_classes = np.unique(y_test)
+                    n_test_classes = len(unique_test_classes)
+
+                    # Skip fold if we don't have at least 2 classes in test set
+                    if n_test_classes < 2:
+                        warnings.warn(
+                            f"Fold {fold_idx}: Test set has only {n_test_classes} class(es). "
+                            f"Skipping this fold for ROC-AUC calculation."
                         )
-            if np.isnan(res["test_score"]).any():
+                        fold_scores.append(np.nan)
-                if not self.ignore_nan:
+                        fold_times.append(np.nan)
-                    print(res["test_score"])
+                        fold_estimators.append(None)
-                    raise ValueError("NaN in results")
+                        continue
-                results = res["test_score"][~np.isnan(res["test_score"])]
+
+                    # Apply IWSS feature selection if enabled
+                    if self.iwss:
+                        # transformer = (
+                        #     MUFS(discrete=False)
+                        #     if "cli_rad" in name
+                        #     else MUFS(discrete=True)
+                        # )
+                        # transformer.iwss(X_train, y_train, 0.5)
+                        # selected_features = transformer.get_results()
+                        # Apply L1-based feature selection
+                        # Using LinearSVC with L1 penalty
+                        lsvc = LinearSVC(
+                            C=0.1,  # Regularization parameter - adjust this for more/fewer features
+                            penalty="l1",
+                            dual=False,
+                            max_iter=2000,
+                            random_state=random_state,
+                        )
+                        selector = SelectFromModel(lsvc, prefit=False)
+                        selector.fit(X_train, y_train)
+
+                        # Transform the data
+                        X_train_selected = selector.transform(X_train)
+                        X_test_selected = selector.transform(X_test)
+
+                        # Get information about selected features
+                        selected_features = selector.get_support(indices=True)
+                        n_selected = len(selected_features)
+                        if len(selected_features) == 0:
+                            warnings.warn(
+                                f"Fold {fold_idx}: No features selected by IWSS. Using all features."
+                            )
+                            X_train_selected = X_train
+                            X_test_selected = X_test
                         else:
-                results = res["test_score"]
+                            X_train_selected = X_train[:, selected_features]
-            self.scores.extend(results)
+                            X_test_selected = X_test[:, selected_features]
-            self.times.extend(res["fit_time"])
+                    else:
-            for result_item in res["estimator"]:
+                        X_train_selected = X_train
-                nodes_item, leaves_item, depth_item = Models.get_complexity(
+                        X_test_selected = X_test
-                    self.model_name, result_item
+
+                    # Clone and fit classifier
+                    clf_fold = clone(clf)
+
+                    start_time = time.time()
+                    clf_fold.fit(X_train_selected, y_train)
+                    fit_time = time.time() - start_time
+
+                    # Get probability predictions
+                    y_proba = clf_fold.predict_proba(X_test_selected)
+
+                    # Calculate ROC-AUC score
+                    # Handle case where test set doesn't have all classes
+                    if len(clf_fold.classes_) != len(unique_test_classes):
+                        # Map probabilities to only test classes
+                        test_class_indices = [
+                            np.where(clf_fold.classes_ == c)[0][0]
+                            for c in unique_test_classes
+                            if c in clf_fold.classes_
+                        ]
+                        y_proba = y_proba[:, test_class_indices]
+
+                    # Binarize labels for multi-class ROC-AUC
+                    y_test_binarized = label_binarize(
+                        y_test, classes=unique_test_classes
+                    )
+
+                    # Calculate ROC-AUC with OVR strategy
+                    if n_test_classes == 2:
+                        # Binary classification
+                        test_score = roc_auc_score(y_test, y_proba[:, 1])
+                    else:
+                        # Multi-class with macro-average
+                        test_score = roc_auc_score(
+                            y_test_binarized,
+                            y_proba,
+                            multi_class="ovr",
+                            average="macro",
+                        )
+
+                    fold_scores.append(test_score)
+                    fold_times.append(fit_time)
+                    fold_estimators.append(clf_fold)
+
+                # Filter out NaN scores if ignore_nan is True
+                scores_array = np.array(fold_scores)
+                times_array = np.array(fold_times)
+
+                if np.isnan(scores_array).any():
+                    if not self.ignore_nan:
+                        nan_folds = np.where(np.isnan(scores_array))[0]
+                        raise ValueError(
+                            f"NaN scores in folds {nan_folds}. "
+                            f"Set ignore_nan=True to skip these folds."
+                        )
+                    else:
+                        # Filter out NaN values
+                        valid_mask = ~np.isnan(scores_array)
+                        scores_array = scores_array[valid_mask]
+                        times_array = times_array[valid_mask]
+                        fold_estimators = [
+                            e
+                            for e, valid in zip(fold_estimators, valid_mask)
+                            if valid
+                        ]
+
+                        if len(scores_array) == 0:
+                            warnings.warn(
+                                f"All folds resulted in NaN for seed {random_state}. Skipping."
+                            )
+                            continue
+
+                # Store results
+                self.scores.extend(scores_array)
+                self.times.extend(times_array)
+
+                # Store complexity metrics
+                for estimator in fold_estimators:
+                    if estimator is not None:
+                        nodes_item, leaves_item, depth_item = (
+                            Models.get_complexity(self.model_name, estimator)
                         )
                         self.nodes.append(nodes_item)
                         self.leaves.append(leaves_item)

benchmark/Models.py

@@ -71,6 +71,7 @@ class Models:
                 algorithm="SAMME",
                 random_state=random_state,
             ),
+            "AdaBoost": AdaBoostClassifier(random_state=random_state),
             "GBC": GradientBoostingClassifier(random_state=random_state),
             "RandomForest": RandomForestClassifier(random_state=random_state),
             "Mock": MockModel(random_state=random_state),
@@ -99,13 +100,13 @@ class Models:
             nodes = 0
             leaves = result.get_n_leaves()
             depth = 0
-        elif name.startswith("Bagging") or name.startswith("AdaBoost"):
+        elif name.startswith("Bagging") or name == "AdaBoostStree":
             nodes, leaves = list(
                 zip(*[x.nodes_leaves() for x in result.estimators_])
             )
             nodes, leaves = mean(nodes), mean(leaves)
             depth = mean([x.depth_ for x in result.estimators_])
-        elif name == "RandomForest":
+        elif name == "RandomForest" or name == "AdaBoost":
             leaves = mean([x.get_n_leaves() for x in result.estimators_])
             depth = mean([x.get_depth() for x in result.estimators_])
             nodes = mean([x.tree_.node_count for x in result.estimators_])

benchmark/ResultsBase.py

@@ -108,10 +108,12 @@ class BaseReport(abc.ABC):
                     status = (
                         Symbols.cross
                         if accuracy <= max_value
-                        else Symbols.upward_arrow
+                        else (
+                            Symbols.upward_arrow
                             if accuracy > max_value
                             else " "
                         )
+                    )
         if status != " ":
             if status not in self._compare_totals:
                 self._compare_totals[status] = 1
@@ -161,6 +163,11 @@ class StubReport(BaseReport):
     def header(self) -> None:
         self.title = self.data["title"]
         self.duration = self.data["duration"]
+        self.model = self.data["model"]
+        self.date = self.data["date"]
+        self.time = self.data["time"]
+        self.metric = self.data["score_name"]
+        self.platform = self.data["platform"]
 
     def footer(self, accuracy: float) -> None:
         self.accuracy = accuracy
@@ -195,9 +202,11 @@ class Summary:
                 self.models.add(model)
                 report = StubReport(
                     os.path.join(
+                        (
                             Folders.hidden_results
                             if self.hidden
-                        else Folders.results,
+                            else Folders.results
+                        ),
                         result,
                     )
                 )

benchmark/__init__.py

@@ -10,7 +10,7 @@ from .Results import Report
 from ._version import __version__
 
 __author__ = "Ricardo Montañana Gómez"
-__copyright__ = "Copyright 2020-2023, Ricardo Montañana Gómez"
+__copyright__ = "Copyright 2020-2024, Ricardo Montañana Gómez"
 __license__ = "MIT License"
 __author_email__ = "ricardo.montanana@alu.uclm.es"
 

benchmark/_version.py

@@ -1 +1 @@
-__version__ = "0.5.0"
+__version__ = "1.0.1"

benchmark/scripts/app/templates/partials/table_report_bootstrap.html

@@ -88,7 +88,7 @@
         <button type="button"
                 class="btn-close"
                 aria-label="Close"
-                onclick="location.href = '/index/{{ compare }}'"></button>
+                onclick="location.href = '{{ back }}'"></button>
         <h7>
         <b>
           Total score: {{ "%.6f" % (data.results | sum(attribute="score") ) }}

benchmark/scripts/app/templates/partials/table_report_bulma.html

@@ -90,7 +90,7 @@
         {% endif %}
         <h2 class="has-text-white has-background-primary">
           <b>
-            <button class="delete" onclick="location.href = '/index/{{ compare }}'"></button>
+            <button class="delete" onclick="location.href = '{{ back }}'"></button>
             Total score: {{ "%.6f" % (data.results | sum(attribute="score") ) }}
           </b>
         </h2>

benchmark/scripts/be_main.py

@@ -14,7 +14,7 @@ def main(args_test=None):
     arguments.xset("stratified").xset("score").xset("model", mandatory=True)
     arguments.xset("n_folds").xset("platform").xset("quiet").xset("title")
     arguments.xset("report").xset("ignore_nan").xset("discretize")
-    arguments.xset("fit_features")
+    arguments.xset("fit_features").xset("iwss")
     arguments.add_exclusive(
         ["grid_paramfile", "best_paramfile", "hyperparameters"]
     )
@@ -43,6 +43,7 @@ def main(args_test=None):
             folds=args.n_folds,
             fit_features=args.fit_features,
             discretize=args.discretize,
+            iwss=args.iwss,
         )
         job.do_experiment()
     except ValueError as e:

benchmark/tests/Arguments_test.py

@@ -68,7 +68,7 @@ class ArgumentsTest(TestBase):
         test_args = ["-n", "3", "-k", "date"]
         with self.assertRaises(SystemExit):
             arguments.parse(test_args)
-        self.assertRegexpMatches(
+        self.assertRegex(
             stderr.getvalue(),
             r"error: the following arguments are required: -m/--model",
         )
@@ -79,7 +79,7 @@ class ArgumentsTest(TestBase):
         test_args = ["-n", "3", "-m", "SVC"]
         with self.assertRaises(SystemExit):
             arguments.parse(test_args)
-        self.assertRegexpMatches(
+        self.assertRegex(
             stderr.getvalue(),
             r"error: the following arguments are required: -k/--key",
         )
@@ -114,7 +114,7 @@ class ArgumentsTest(TestBase):
         test_args = None
         with self.assertRaises(SystemExit):
             arguments.parse(test_args)
-        self.assertRegexpMatches(
+        self.assertRegex(
             stderr.getvalue(),
             r"error: the following arguments are required: -m/--model, "
             "-k/--key, --title",

benchmark/tests/Models_test.py

@@ -102,7 +102,7 @@ class ModelTest(TestBase):
         test = {
             "STree": ((11, 6, 4), 1.0),
             "Wodt": ((303, 152, 50), 0.9382022471910112),
-            "ODTE": ((7.86, 4.43, 3.37), 1.0),
+            "ODTE": ((786, 443, 337), 1.0),
             "Cart": ((23, 12, 5), 1.0),
             "SVC": ((0, 0, 0), 0.7078651685393258),
             "RandomForest": ((21.3, 11, 5.26), 1.0),

benchmark/tests/datasets/all.txt

@@ -1,2 +1,2 @@
-iris,class,all
+iris;class;all
-wine,class,[0, 1]
+wine;class;[0, 1]

benchmark/tests/results/grid_output_accuracy_STree.json

@@ -6,7 +6,7 @@
             "kernel": "liblinear",
             "multiclass_strategy": "ovr"
         },
-        "v. 1.3.1, Computed on Test on 2022-02-22 at 12:00:00 took 1s"
+        "v. 1.4.0, Computed on Test on 2022-02-22 at 12:00:00 took 1s"
     ],
     "balloons": [
         0.625,
@@ -15,6 +15,6 @@
             "kernel": "linear",
             "multiclass_strategy": "ovr"
         },
-        "v. 1.3.1, Computed on Test on 2022-02-22 at 12:00:00 took 1s"
+        "v. 1.4.0, Computed on Test on 2022-02-22 at 12:00:00 took 1s"
     ]
 }

benchmark/tests/scripts/Be_Main_test.py

@@ -120,7 +120,7 @@ class BeMainTest(TestBase):
                 module.main(parameter)
             self.assertEqual(msg.exception.code, 2)
             self.assertEqual(stderr.getvalue(), "")
-            self.assertRegexpMatches(stdout.getvalue(), message)
+            self.assertRegex(stdout.getvalue(), message)
 
     def test_be_main_best_params_non_existent(self):
         model = "GBC"

benchmark/tests/test_files/exreport_excel_Datasets.test

@@ -1,4 +1,4 @@
-1;1;"Datasets used in benchmark ver. 0.5.0"
+1;1;"Datasets used in benchmark ver. 1.0.1"
 2;1;" Default score accuracy"
 2;2;"Cross validation"
 2;6;"5 Folds"

benchmark/tests/test_files/report_datasets.test

@@ -1,4 +1,4 @@
-Datasets used in benchmark ver. 0.5.0
+Datasets used in benchmark ver. 1.0.1
 
 Dataset                        Sampl. Feat. Cont Cls Balance
 ============================== ====== ===== ==== === ==========================================