Merge remote-tracking branch 'origin/main' into mm/estimator-bases

# Conflicts:
#	aeon/clustering/base.py

Author: MatthewMiddlehurst

README.md

@@ -139,6 +139,7 @@ def __init__(
         self.distance_params = distance_params
         self.n_samples = n_samples
         self.n_sampling_iters = n_sampling_iters
+        self.n_clusters = n_clusters
 
         self.cluster_centers_ = None
         self.labels_ = None
@@ -148,7 +149,7 @@ def __init__(
         self._random_state = None
         self._kmedoids_instance = None
 
-        super().__init__(n_clusters)
+        super().__init__()
 
     def _predict(self, X: np.ndarray, y=None) -> np.ndarray:
         return self._kmedoids_instance.predict(X)
@@ -207,9 +208,6 @@ def _fit(self, X: np.ndarray, y=None):
         self.n_iter_ = best_pam.n_iter_
         self._kmedoids_instance = best_pam
 
-    def _score(self, X, y=None):
-        return -self.inertia_
-
     @classmethod
     def _get_test_params(cls, parameter_set="default"):
         """Return testing parameter settings for the estimator.

aeon/clustering/_clara.py

@@ -179,6 +179,7 @@ def __init__(
         self.init = init
         self.sigma_decay_function = sigma_decay_function
         self.custom_alignment_path = custom_alignment_path
+        self.n_clusters = n_clusters
 
         self._random_state = None
         self._alignment_path_callable = None
@@ -191,7 +192,7 @@ def __init__(
 
         self.labels_ = None
         self.cluster_centers_ = None
-        super().__init__(n_clusters=n_clusters)
+        super().__init__()
 
     def _fit(self, X, y=None):
         self._check_params(X)
@@ -219,9 +220,6 @@ def _fit(self, X, y=None):
     def _predict(self, X, y=None):
         return self._find_bmu(X, self.cluster_centers_)
 
-    def _score(self, X, y=None):
-        raise NotImplementedError("TimeSeriesSOM does not support scoring")
-
     def _find_bmu(self, x, weights):
         pairwise_matrix = pairwise_distance(
             x,

aeon/clustering/_elastic_som.py

@@ -192,6 +192,7 @@ def __init__(
         self.distance_params = distance_params
         self.average_params = average_params
         self.averaging_method = averaging_method
+        self.n_clusters = n_clusters
 
         self.cluster_centers_ = None
         self.labels_ = None
@@ -203,7 +204,7 @@ def __init__(
         self._averaging_method = None
         self._average_params = None
 
-        super().__init__(n_clusters)
+        super().__init__()
 
     def _fit(self, X: np.ndarray, y=None):
         self._check_params(X)
@@ -267,7 +268,7 @@ def _fit_one_init(self, X: np.ndarray) -> tuple:
             prev_inertia = curr_inertia
             prev_labels = curr_labels
 
-            if change_in_centres < self.tol:
+            if change_in_centres < self.tol or (i + 1) == self.max_iter:
                 break
 
             # Compute new cluster centres
@@ -281,9 +282,6 @@ def _fit_one_init(self, X: np.ndarray) -> tuple:
 
         return prev_labels, cluster_centres, prev_inertia, i + 1
 
-    def _score(self, X, y=None):
-        return -self.inertia_
-
     def _predict(self, X: np.ndarray, y=None) -> np.ndarray:
         if isinstance(self.distance, str):
             pairwise_matrix = pairwise_distance(

aeon/clustering/_k_means.py

@@ -171,6 +171,7 @@ def __init__(
         self.random_state = random_state
         self.distance_params = distance_params
         self.method = method
+        self.n_clusters = n_clusters
 
         self.cluster_centers_ = None
         self.labels_ = None
@@ -184,7 +185,7 @@ def __init__(
         self._fit_method = None
 
         self._distance_params = {}
-        super().__init__(n_clusters)
+        super().__init__()
 
     def _fit(self, X: np.ndarray, y=None):
         self._check_params(X)
@@ -207,9 +208,6 @@ def _fit(self, X: np.ndarray, y=None):
         self.cluster_centers_ = best_centers
         self.n_iter_ = best_iters
 
-    def _score(self, X, y=None):
-        return -self.inertia_
-
     def _predict(self, X: np.ndarray, y=None) -> np.ndarray:
         if isinstance(self.distance, str):
             pairwise_matrix = pairwise_distance(

aeon/clustering/_k_medoids.py

@@ -89,6 +89,7 @@ def __init__(
         self.tol = tol
         self.verbose = verbose
         self.random_state = random_state
+        self.n_clusters = n_clusters
 
         self.cluster_centers_ = None
         self.labels_ = None
@@ -97,7 +98,7 @@ def __init__(
 
         self._tslearn_k_shapes = None
 
-        super().__init__(n_clusters=n_clusters)
+        super().__init__()
 
     def _fit(self, X, y=None):
         """Fit time series clusterer to training data.
@@ -130,7 +131,7 @@ def _fit(self, X, y=None):
 
         self._tslearn_k_shapes.fit(_X)
         self._cluster_centers = self._tslearn_k_shapes.cluster_centers_
-        self.labels_ = self._tslearn_k_shapes.labels_
+        self.labels_ = self._tslearn_k_shapes.predict(_X)
         self.inertia_ = self._tslearn_k_shapes.inertia_
         self.n_iter_ = self._tslearn_k_shapes.n_iter_
 
@@ -179,6 +180,3 @@ def _get_test_params(cls, parameter_set="default"):
             "verbose": False,
             "random_state": 1,
         }
-
-    def _score(self, X, y=None):
-        return np.abs(self.inertia_)

aeon/clustering/_k_shape.py

@@ -90,6 +90,7 @@ def __init__(
         self.tol = tol
         self.verbose = verbose
         self.random_state = random_state
+        self.n_clusters = n_clusters
 
         self.cluster_centers_ = None
         self.labels_ = None
@@ -98,7 +99,7 @@ def __init__(
 
         self._tslearn_k_shapes = None
 
-        super().__init__(n_clusters=n_clusters)
+        super().__init__()
 
     def _fit(self, X, y=None):
         """Fit time series clusterer to training data.
@@ -131,7 +132,7 @@ def _fit(self, X, y=None):
 
         self._tslearn_k_shapes.fit(_X)
         self._cluster_centers = self._tslearn_k_shapes.cluster_centers_
-        self.labels_ = self._tslearn_k_shapes.labels_
+        self.labels_ = self._tslearn_k_shapes.predict(_X)
         self.inertia_ = self._tslearn_k_shapes.inertia_
         self.n_iter_ = self._tslearn_k_shapes.n_iter_
 
@@ -180,6 +181,3 @@ def _get_test_params(cls, parameter_set="default"):
             "verbose": False,
             "random_state": 1,
         }
-
-    def _score(self, X, y=None):
-        return np.abs(self.inertia_)

aeon/clustering/_k_shapes.py

@@ -108,6 +108,7 @@ def __init__(
         self.verbose = verbose
         self.n_jobs = n_jobs
         self.random_state = random_state
+        self.n_clusters = n_clusters
 
         self.cluster_centers_ = None
         self.labels_ = None
@@ -116,7 +117,7 @@ def __init__(
 
         self._tslearn_kernel_k_means = None
 
-        super().__init__(n_clusters=n_clusters)
+        super().__init__()
 
     def _fit(self, X, y=None):
         """Fit time series clusterer to training data.
@@ -204,6 +205,3 @@ def _get_test_params(cls, parameter_set="default") -> dict:
             "n_jobs": 1,
             "random_state": 1,
         }
-
-    def _score(self, X, y=None) -> float:
-        return np.abs(self.inertia_)

aeon/clustering/_kernel_k_means.py

@@ -1,7 +1,5 @@
 """Base class for clustering."""
 
-from typing import Optional
-
 __maintainer__ = []
 __all__ = ["BaseClusterer"]
 
@@ -27,8 +25,7 @@ class BaseClusterer(BaseCollectionEstimator):
     }
 
     @abstractmethod
-    def __init__(self, n_clusters: Optional[int] = None):
-        self.n_clusters = n_clusters
+    def __init__(self):
         # required for compatibility with some sklearn interfaces e.g.
         # CalibratedClassifierCV
         self._estimator_type = "clusterer"
@@ -121,6 +118,7 @@ def predict_proba(self, X) -> np.ndarray:
         self._check_shape(X)
         return self._predict_proba(X)
 
+    @final
     def fit_predict(self, X, y=None) -> np.ndarray:
         """Compute cluster centers and predict cluster index for each time series.
 
@@ -139,11 +137,10 @@ def fit_predict(self, X, y=None) -> np.ndarray:
         np.ndarray (1d array of shape (n_cases,))
             Index of the cluster each time series in X belongs to.
         """
-        self.fit(X)
-        return self.predict(X)
+        return self._fit_predict(X, y)
 
-    def score(self, X, y=None) -> float:
-        """Score the quality of the clusterer.
+    def _fit_predict(self, X, y=None) -> np.ndarray:
+        """Fit predict using base methods.
 
         Parameters
         ----------
@@ -155,13 +152,11 @@ def score(self, X, y=None) -> float:
 
         Returns
         -------
-        score : float
-            Score of the clusterer.
+        np.ndarray (1d array of shape (n_cases,))
+            Index of the cluster each time series in X belongs to.
         """
-        self._check_is_fitted()
-        X = self._preprocess_collection(X, store_metadata=False)
-        self._check_shape(X)
-        return self._score(X, y)
+        self.fit(X)
+        return self.labels_
 
     def _predict_proba(self, X) -> np.ndarray:
         """Predicts labels probabilities for sequences in X.
@@ -194,17 +189,17 @@ def _predict_proba(self, X) -> np.ndarray:
         for i, u in enumerate(unique):
             preds[preds == u] = i
         n_cases = len(preds)
-        n_clusters = self.n_clusters
+        if hasattr(self, "n_clusters"):
+            n_clusters = self.n_clusters
+        else:
+            n_clusters = len(np.unique(preds))
         if n_clusters is None:
             n_clusters = int(max(preds)) + 1
-        dists = np.zeros((X.shape[0], n_clusters))
+        dists = np.zeros((len(X), n_clusters))
         for i in range(n_cases):
             dists[i, preds[i]] = 1
         return dists
 
-    @abstractmethod
-    def _score(self, X, y=None): ...
-
     @abstractmethod
     def _predict(self, X) -> np.ndarray:
         """Predict the closest cluster each sample in X belongs to.

aeon/clustering/base.py

@@ -86,10 +86,9 @@ def __init__(self, transformers, clusterer, random_state=None):
         )
 
     def _fit(self, X, y=None):
-        return super()._fit(X, y)
-
-    def _score(self, X, y=None):
-        raise NotImplementedError("Pipeline does not support scoring.")
+        super()._fit(X, y)
+        self.labels_ = self.steps_[-1][1].labels_
+        return self
 
     @classmethod
     def _get_test_params(cls, parameter_set="default"):

aeon/clustering/compose/_pipeline.py

@@ -20,8 +20,6 @@ class AEAttentionBiGRUClusterer(BaseDeepClusterer):
 
     Parameters
     ----------
-    n_clusters : int, default=None
-        Number of clusters for the deep learnign model.
     clustering_algorithm : str, default="deprecated"
         Use 'estimator' parameter instead.
     clustering_params : dict, default=None
@@ -106,7 +104,6 @@ class AEAttentionBiGRUClusterer(BaseDeepClusterer):
 
     def __init__(
         self,
-        n_clusters=None,
         estimator=None,
         clustering_algorithm="deprecated",
         clustering_params=None,
@@ -153,7 +150,6 @@ def __init__(
         self.random_state = random_state
 
         super().__init__(
-            n_clusters=n_clusters,
             clustering_algorithm=clustering_algorithm,
             clustering_params=clustering_params,
             estimator=estimator,
@@ -302,12 +298,6 @@ def _fit(self, X):
 
         return self
 
-    def _score(self, X, y=None):
-        # Transpose to conform to Keras input style.
-        X = X.transpose(0, 2, 1)
-        latent_space = self.model_.layers[1].predict(X)
-        return self._estimator.score(latent_space)
-
     @classmethod
     def _get_test_params(cls, parameter_set="default"):
         """Return testing parameter settings for the estimator.

aeon/clustering/deep_learning/_ae_abgru.py

@@ -20,8 +20,6 @@ class AEBiGRUClusterer(BaseDeepClusterer):
 
     Parameters
     ----------
-    n_clusters : int, default=None
-        Number of clusters for the deep learnign model.
     clustering_algorithm : str, default="deprecated"
         Use 'estimator' parameter instead.
     clustering_params : dict, default=None
@@ -105,7 +103,6 @@ class AEBiGRUClusterer(BaseDeepClusterer):
 
     def __init__(
         self,
-        n_clusters=None,
         clustering_algorithm="deprecated",
         estimator=None,
         clustering_params=None,
@@ -152,7 +149,6 @@ def __init__(
         self.random_state = random_state
 
         super().__init__(
-            n_clusters=n_clusters,
             clustering_algorithm=clustering_algorithm,
             clustering_params=clustering_params,
             estimator=estimator,
@@ -300,12 +296,6 @@ def _fit(self, X):
 
         return self
 
-    def _score(self, X, y=None):
-        # Transpose to conform to Keras input style.
-        X = X.transpose(0, 2, 1)
-        latent_space = self.model_.layers[1].predict(X)
-        return self._estimator.score(latent_space)
-
     @classmethod
     def _get_test_params(cls, parameter_set="default"):
         """Return testing parameter settings for the estimator.