scikit-learn-intelex 2024.0.1__py311-none-manylinux1_x86_64.whl → 2024.2.0__py311-none-manylinux1_x86_64.whl

{scikit_learn_intelex-2024.0.1.dist-info → scikit_learn_intelex-2024.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-learn-intelex
-Version: 2024.0.1
+Version: 2024.2.0
 Summary: Intel(R) Extension for Scikit-learn is a seamless way to speed up your Scikit-learn application.
 Home-page: https://github.com/intel/scikit-learn-intelex
 Author: Intel Corporation
@@ -31,7 +31,7 @@ Classifier: Topic :: Software Development
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: daal4py (==2024.0.1)
+Requires-Dist: daal4py (==2024.2.0)
 Requires-Dist: scikit-learn (>=0.22)
 
 

scikit_learn_intelex-2024.2.0.dist-info/RECORD

@@ -0,0 +1,101 @@
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+scikit_learn_intelex-2024.2.0.dist-info/top_level.txt,sha256=kzKChSWGJEYFmdj5PwE63HNuP_PVOhWfD32ytH9rL9Q,10
+scikit_learn_intelex-2024.2.0.dist-info/RECORD,,

sklearnex/__init__.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ==============================================================================
 # Copyright 2021 Intel Corporation
 #
@@ -15,6 +14,8 @@
 # limitations under the License.
 # ==============================================================================
 
+from onedal.common.hyperparameters import get_hyperparameters
+
 from . import utils
 from ._config import config_context, get_config, set_config
 from .dispatcher import (
@@ -33,6 +34,7 @@ __all__ = [
     "decomposition",
     "ensemble",
     "get_config",
+    "get_hyperparameters",
     "get_patch_map",
     "get_patch_names",
     "is_patched_instance",

sklearnex/__main__.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ==============================================================================
 # Copyright 2021 Intel Corporation
 #

sklearnex/_utils.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ===============================================================================
 # Copyright 2021 Intel Corporation
 #
@@ -93,3 +92,18 @@ def get_patch_message(s, queue=None):
 
 def get_sklearnex_version(rule):
     return daal_check_version(rule)
+
+
+def register_hyperparameters(hyperparameters_map):
+    """Decorator for hyperparameters support in estimator class.
+    Adds `get_hyperparameters` method to class.
+    """
+
+    def wrap_class(estimator_class):
+        def get_hyperparameters(self, op):
+            return hyperparameters_map[op]
+
+        estimator_class.get_hyperparameters = get_hyperparameters
+        return estimator_class
+
+    return wrap_class

sklearnex/basic_statistics/__init__.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ==============================================================================
 # Copyright 2023 Intel Corporation
 #

sklearnex/cluster/__init__.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ===============================================================================
 # Copyright 2021 Intel Corporation
 #

sklearnex/cluster/dbscan.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ===============================================================================
 # Copyright 2021 Intel Corporation
 #
@@ -23,6 +22,7 @@ from scipy import sparse as sp
 from sklearn.cluster import DBSCAN as sklearn_DBSCAN
 from sklearn.utils.validation import _check_sample_weight
 
+from daal4py.sklearn._n_jobs_support import control_n_jobs
 from daal4py.sklearn._utils import sklearn_check_version
 from onedal.cluster import DBSCAN as onedal_DBSCAN
 
@@ -46,6 +46,7 @@ class BaseDBSCAN(ABC):
         self.n_features_in_ = self._onedal_estimator.n_features_in_
 
 
+@control_n_jobs(decorated_methods=["fit"])
 class DBSCAN(sklearn_DBSCAN, BaseDBSCAN):
     __doc__ = sklearn_DBSCAN.__doc__
 

sklearnex/cluster/k_means.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ===============================================================================
 # Copyright 2021 Intel Corporation
 #

sklearnex/cluster/tests/test_dbscan.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ===============================================================================
 # Copyright 2021 Intel Corporation
 #

sklearnex/cluster/tests/test_kmeans.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ===============================================================================
 # Copyright 2021 Intel Corporation
 #

sklearnex/covariance/__init__.py

@@ -0,0 +1,19 @@
+# ===============================================================================
+# Copyright 2024 Intel Corporation
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ===============================================================================
+
+from .incremental_covariance import IncrementalEmpiricalCovariance
+
+__all__ = ["IncrementalEmpiricalCovariance"]

sklearnex/covariance/incremental_covariance.py

@@ -0,0 +1,130 @@
+# ===============================================================================
+# Copyright 2024 Intel Corporation
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ===============================================================================
+
+import numpy as np
+from sklearn.utils import check_array, gen_batches
+
+from daal4py.sklearn._n_jobs_support import control_n_jobs
+from onedal._device_offload import support_usm_ndarray
+from onedal.covariance import (
+    IncrementalEmpiricalCovariance as onedal_IncrementalEmpiricalCovariance,
+)
+
+
+@control_n_jobs(decorated_methods=["partial_fit"])
+class IncrementalEmpiricalCovariance:
+    """
+    Incremental estimator for covariance.
+    Allows to compute empirical covariance estimated by maximum
+    likelihood method if data are splitted into batches.
+
+    Parameters
+    ----------
+    batch_size : int, default=None
+        The number of samples to use for each batch. Only used when calling
+        ``fit``. If ``batch_size`` is ``None``, then ``batch_size``
+        is inferred from the data and set to ``5 * n_features``, to provide a
+        balance between approximation accuracy and memory consumption.
+
+    Attributes
+    ----------
+    location_ : ndarray of shape (n_features,)
+        Estimated location, i.e. the estimated mean.
+
+    covariance_ : ndarray of shape (n_features, n_features)
+        Estimated covariance matrix
+    """
+
+    _onedal_incremental_covariance = staticmethod(onedal_IncrementalEmpiricalCovariance)
+
+    def __init__(self, batch_size=None):
+        self._need_to_finalize = False  # If True then finalize compute should
+        #      be called to obtain covariance_ or location_ from partial compute data
+        self.batch_size = batch_size
+
+    def _onedal_finalize_fit(self):
+        assert hasattr(self, "_onedal_estimator")
+        self._onedal_estimator.finalize_fit()
+        self._need_to_finalize = False
+
+    def _onedal_partial_fit(self, X, queue):
+        onedal_params = {
+            "method": "dense",
+            "bias": True,
+        }
+        if not hasattr(self, "_onedal_estimator"):
+            self._onedal_estimator = self._onedal_incremental_covariance(**onedal_params)
+        self._onedal_estimator.partial_fit(X, queue)
+        self._need_to_finalize = True
+
+    @property
+    def covariance_(self):
+        if self._need_to_finalize:
+            self._onedal_finalize_fit()
+        return self._onedal_estimator.covariance_
+
+    @property
+    def location_(self):
+        if self._need_to_finalize:
+            self._onedal_finalize_fit()
+        return self._onedal_estimator.location_
+
+    @support_usm_ndarray()
+    def partial_fit(self, X, queue=None):
+        """
+        Incremental fit with X. All of X is processed as a single batch.
+
+        Parameters
+        ----------
+        X : array-like of shape (n_samples, n_features)
+            Training data, where `n_samples` is the number of samples and
+            `n_features` is the number of features.
+
+        Returns
+        -------
+        self : object
+            Returns the instance itself.
+        """
+        X = check_array(X, dtype=[np.float64, np.float32])
+        self._onedal_partial_fit(X, queue)
+        return self
+
+    def fit(self, X, queue=None):
+        """
+        Fit the model with X, using minibatches of size batch_size.
+
+        Parameters
+        ----------
+        X : array-like of shape (n_samples, n_features)
+            Training data, where `n_samples` is the number of samples and
+            `n_features` is the number of features.
+
+        Returns
+        -------
+        self : object
+            Returns the instance itself.
+        """
+        n_samples, n_features = X.shape
+        if self.batch_size is None:
+            batch_size_ = 5 * n_features
+        else:
+            batch_size_ = self.batch_size
+        for batch in gen_batches(n_samples, batch_size_):
+            X_batch = X[batch]
+            self.partial_fit(X_batch, queue=queue)
+
+        self._onedal_finalize_fit()
+        return self

sklearnex/covariance/tests/test_incremental_covariance.py

@@ -0,0 +1,143 @@
+# ===============================================================================
+# Copyright 2024 Intel Corporation
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ===============================================================================
+
+import numpy as np
+import pytest
+from numpy.testing import assert_allclose
+
+from onedal.tests.utils._dataframes_support import (
+    _convert_to_dataframe,
+    get_dataframes_and_queues,
+)
+
+
+@pytest.mark.parametrize("dataframe,queue", get_dataframes_and_queues())
+@pytest.mark.parametrize("dtype", [np.float32, np.float64])
+def test_sklearnex_partial_fit_on_gold_data(dataframe, queue, dtype):
+    from sklearnex.covariance import IncrementalEmpiricalCovariance
+
+    X = np.array([[0, 1], [0, 1]])
+    X = X.astype(dtype)
+    X_split = np.array_split(X, 2)
+    inccov = IncrementalEmpiricalCovariance()
+
+    for i in range(2):
+        X_split_df = _convert_to_dataframe(
+            X_split[i], sycl_queue=queue, target_df=dataframe
+        )
+        result = inccov.partial_fit(X_split_df)
+
+    expected_covariance = np.array([[0, 0], [0, 0]])
+    expected_means = np.array([0, 1])
+
+    assert_allclose(expected_covariance, result.covariance_)
+    assert_allclose(expected_means, result.location_)
+
+    X = np.array([[1, 2], [3, 6]])
+    X = X.astype(dtype)
+    X_split = np.array_split(X, 2)
+    inccov = IncrementalEmpiricalCovariance()
+
+    for i in range(2):
+        X_split_df = _convert_to_dataframe(
+            X_split[i], sycl_queue=queue, target_df=dataframe
+        )
+        result = inccov.partial_fit(X_split_df)
+
+    expected_covariance = np.array([[1, 2], [2, 4]])
+    expected_means = np.array([2, 4])
+
+    assert_allclose(expected_covariance, result.covariance_)
+    assert_allclose(expected_means, result.location_)
+
+
+@pytest.mark.parametrize("dataframe,queue", get_dataframes_and_queues())
+@pytest.mark.parametrize("batch_size", [2, 4])
+@pytest.mark.parametrize("dtype", [np.float32, np.float64])
+def test_sklearnex_fit_on_gold_data(dataframe, queue, batch_size, dtype):
+    from sklearnex.covariance import IncrementalEmpiricalCovariance
+
+    X = np.array([[0, 1, 2, 3], [0, -1, -2, -3], [0, 1, 2, 3], [0, 1, 2, 3]])
+    X = X.astype(dtype)
+    X_df = _convert_to_dataframe(X, sycl_queue=queue, target_df=dataframe)
+    inccov = IncrementalEmpiricalCovariance(batch_size=batch_size)
+
+    result = inccov.fit(X_df)
+
+    expected_covariance = np.array(
+        [[0, 0, 0, 0], [0, 0.75, 1.5, 2.25], [0, 1.5, 3, 4.5], [0, 2.25, 4.5, 6.75]]
+    )
+    expected_means = np.array([0, 0.5, 1, 1.5])
+
+    assert_allclose(expected_covariance, result.covariance_)
+    assert_allclose(expected_means, result.location_)
+
+
+@pytest.mark.parametrize("dataframe,queue", get_dataframes_and_queues())
+@pytest.mark.parametrize("num_batches", [2, 4, 6, 8, 10])
+@pytest.mark.parametrize("row_count", [100, 1000, 2000])
+@pytest.mark.parametrize("column_count", [10, 100, 200])
+@pytest.mark.parametrize("dtype", [np.float32, np.float64])
+def test_sklearnex_partial_fit_on_random_data(
+    dataframe, queue, num_batches, row_count, column_count, dtype
+):
+    from sklearnex.covariance import IncrementalEmpiricalCovariance
+
+    seed = 77
+    gen = np.random.default_rng(seed)
+    X = gen.uniform(low=-0.3, high=+0.7, size=(row_count, column_count))
+    X = X.astype(dtype)
+    X_split = np.array_split(X, num_batches)
+    inccov = IncrementalEmpiricalCovariance()
+
+    for i in range(num_batches):
+        X_split_df = _convert_to_dataframe(
+            X_split[i], sycl_queue=queue, target_df=dataframe
+        )
+        result = inccov.partial_fit(X_split_df)
+
+    expected_covariance = np.cov(X.T, bias=1)
+    expected_means = np.mean(X, axis=0)
+
+    assert_allclose(expected_covariance, result.covariance_, atol=1e-6)
+    assert_allclose(expected_means, result.location_, atol=1e-6)
+
+
+@pytest.mark.parametrize("dataframe,queue", get_dataframes_and_queues())
+@pytest.mark.parametrize("num_batches", [2, 4, 6, 8, 10])
+@pytest.mark.parametrize("row_count", [100, 1000, 2000])
+@pytest.mark.parametrize("column_count", [10, 100, 200])
+@pytest.mark.parametrize("dtype", [np.float32, np.float64])
+def test_sklearnex_fit_on_random_data(
+    dataframe, queue, num_batches, row_count, column_count, dtype
+):
+    from sklearnex.covariance import IncrementalEmpiricalCovariance
+
+    seed = 77
+    gen = np.random.default_rng(seed)
+    X = gen.uniform(low=-0.3, high=+0.7, size=(row_count, column_count))
+    X = X.astype(dtype)
+    X_df = _convert_to_dataframe(X, sycl_queue=queue, target_df=dataframe)
+    batch_size = row_count // num_batches
+    inccov = IncrementalEmpiricalCovariance(batch_size=batch_size)
+
+    result = inccov.fit(X_df)
+
+    expected_covariance = np.cov(X.T, bias=1)
+    expected_means = np.mean(X, axis=0)
+
+    assert_allclose(expected_covariance, result.covariance_, atol=1e-6)
+    assert_allclose(expected_means, result.location_, atol=1e-6)

sklearnex/decomposition/__init__.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ===============================================================================
 # Copyright 2021 Intel Corporation
 #

sklearnex/decomposition/pca.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ===============================================================================
 # Copyright 2021 Intel Corporation
 #

sklearnex/decomposition/tests/test_pca.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ===============================================================================
 # Copyright 2023 Intel Corporation
 #

sklearnex/dispatcher.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ==============================================================================
 # Copyright 2021 Intel Corporation
 #
@@ -42,6 +41,7 @@ def get_patch_map():
         # Scikit-learn* modules
         import sklearn as base_module
         import sklearn.cluster as cluster_module
+        import sklearn.covariance as covariance_module
         import sklearn.decomposition as decomposition_module
         import sklearn.ensemble as ensemble_module
         import sklearn.linear_model as linear_model_module
@@ -69,6 +69,7 @@ def get_patch_map():
         from .ensemble import RandomForestClassifier as RandomForestClassifier_sklearnex
         from .ensemble import RandomForestRegressor as RandomForestRegressor_sklearnex
         from .linear_model import LinearRegression as LinearRegression_sklearnex
+        from .linear_model import LogisticRegression as LogisticRegression_sklearnex
         from .neighbors import KNeighborsClassifier as KNeighborsClassifier_sklearnex
         from .neighbors import KNeighborsRegressor as KNeighborsRegressor_sklearnex
         from .neighbors import LocalOutlierFactor as LocalOutlierFactor_sklearnex
@@ -76,6 +77,9 @@ def get_patch_map():
 
         # Preview classes for patching
         from .preview.cluster import KMeans as KMeans_sklearnex
+        from .preview.covariance import (
+            EmpiricalCovariance as EmpiricalCovariance_sklearnex,
+        )
         from .preview.decomposition import PCA as PCA_sklearnex
         from .svm import SVC as SVC_sklearnex
         from .svm import SVR as SVR_sklearnex
@@ -101,6 +105,18 @@ def get_patch_map():
                 ]
             ]
 
+            # Covariance
+            mapping["empiricalcovariance"] = [
+                [
+                    (
+                        covariance_module,
+                        "EmpiricalCovariance",
+                        EmpiricalCovariance_sklearnex,
+                    ),
+                    None,
+                ]
+            ]
+
         # DBSCAN
         mapping.pop("dbscan")
         mapping["dbscan"] = [[(cluster_module, "DBSCAN", DBSCAN_sklearnex), None]]
@@ -128,6 +144,24 @@ def get_patch_map():
         ]
         mapping["linearregression"] = mapping["linear"]
 
+        # Logistic Regression
+
+        mapping.pop("logisticregression")
+        mapping.pop("log_reg")
+        mapping.pop("logistic")
+        mapping.pop("_logistic_regression_path")
+        mapping["log_reg"] = [
+            [
+                (
+                    linear_model_module,
+                    "LogisticRegression",
+                    LogisticRegression_sklearnex,
+                ),
+                None,
+            ]
+        ]
+        mapping["logisticregression"] = mapping["log_reg"]
+
         # kNN
         mapping.pop("knn_classifier")
         mapping.pop("kneighborsclassifier")

sklearnex/ensemble/__init__.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # ===============================================================================
 # Copyright 2023 Intel Corporation
 #