Merge pull request #6867 from VesnaT/pls_coeffs

PLS: Adjust coeffs to newest sklearn

Orange/widgets/model/owpls.py

@@ -68,15 +68,15 @@ def update_model(self):
 
     def _create_output_coeffs_loadings(self) -> Table:
         intercept = self.model.intercept.T[None, :]
-        coefficients = self.model.coefficients.T
+        coefficients = self.model.coefficients
         _, y_loadings = self.model.loadings
         x_rotations, _ = self.model.rotations
 
-        n_features, n_targets = coefficients.shape
+        n_targets, n_features = coefficients.shape
         n_components = x_rotations.shape[1]
 
         names = [f"coef ({v.name})" for v in self.model.domain.class_vars]
-        names += [f"coef/X_sd ({v.name})" for v in self.model.domain.class_vars]
+        names += [f"coef * X_sd ({v.name})" for v in self.model.domain.class_vars]
         names += [f"w*c {i + 1}" for i in range(n_components)]
         domain = Domain(
             [ContinuousVariable(n) for n in names],
@@ -85,18 +85,16 @@ def _create_output_coeffs_loadings(self) -> Table:
         )
 
         data = self.model.data_to_model_domain(self.data)
-        x_std = np.std(data.X, axis=0)
-        coeffs_x_std = coefficients.T / x_std
-        X_features = np.hstack((coefficients,
-                                coeffs_x_std.T,
+        X_features = np.hstack((coefficients.T,
+                                (coefficients * np.std(data.X, axis=0)).T,
                                 x_rotations))
         X_targets = np.hstack((np.full((n_targets, n_targets), np.nan),
                                np.full((n_targets, n_targets), np.nan),
                                y_loadings))
 
-        coeffs = coeffs_x_std * np.mean(data.X, axis=0)
-        X_intercepts = np.hstack((intercept,
-                                  intercept - coeffs.sum(),
+        coeffs = coefficients * np.mean(data.X, axis=0)
+        X_intercepts = np.hstack((intercept - coeffs.sum(),
+                                  intercept,
                                   np.full((1, n_components), np.nan)))
         X = np.vstack((X_features, X_targets, X_intercepts))
 

Orange/widgets/model/tests/test_owpls.py

@@ -1,5 +1,6 @@
 import unittest
 import numpy as np
+from sklearn.cross_decomposition import PLSRegression
 
 from Orange.data import Table, Domain, StringVariable
 from Orange.widgets.model.owpls import OWPLS
@@ -30,6 +31,19 @@ def setUp(self):
             ParameterMapping('n_components', self.widget.controls.n_components)
         ]
 
+    def test_coeffs_compare_sklearn(self):
+        self.send_signal(self.widget.Inputs.data, self._data)
+        coefsdata = self.get_output(self.widget.Outputs.coefsdata)
+        intercept = coefsdata.X[-1, 0]
+        coeffs = coefsdata.X[:-2, 0]
+        Y_orange = self._data.X @ coeffs + intercept
+
+        pls = PLSRegression(n_components=2)
+        pls.fit(self._data.X, self._data.Y)
+        Y_sklearn = pls.predict(self._data.X)
+
+        np.testing.assert_almost_equal(Y_sklearn, Y_orange)
+
     def test_output_coefsdata(self):
         self.send_signal(self.widget.Inputs.data, self._data)
         coefsdata = self.get_output(self.widget.Outputs.coefsdata)
@@ -38,7 +52,7 @@ def test_output_coefsdata(self):
         self.assertEqual(coefsdata.Y.shape, (15, 0))
         self.assertEqual(coefsdata.metas.shape, (15, 2))
 
-        self.assertEqual(["coef (MEDV)", "coef/X_sd (MEDV)", "w*c 1", "w*c 2"],
+        self.assertEqual(["coef (MEDV)", "coef * X_sd (MEDV)", "w*c 1", "w*c 2"],
                          [v.name for v in coefsdata.domain.attributes])
         self.assertEqual(["Variable name", "Variable role"],
                          [v.name for v in coefsdata.domain.metas])
@@ -47,9 +61,9 @@ def test_output_coefsdata(self):
         self.assertTrue((coefsdata.metas[:-2, 1] == 0).all())
         self.assertTrue((coefsdata.metas[-2, 1] == 1))
         self.assertTrue(np.isnan(coefsdata.metas[-1, 1]))
-        self.assertAlmostEqual(coefsdata.X[0, 2], 0.237, 3)
-        self.assertAlmostEqual(coefsdata.X[13, 2], -0.304, 3)
-        self.assertAlmostEqual(coefsdata.X[-1, 0], 22.5, 1)
+        self.assertAlmostEqual(coefsdata.X[0, 3], 0.012, 3)
+        self.assertAlmostEqual(coefsdata.X[13, 3], 0.389, 3)
+        self.assertAlmostEqual(coefsdata.X[-1, 0], 13.7, 1)
         self.assertTrue(np.isnan(coefsdata.X[-1, 2:]).all())
 
     def test_output_coefsdata_multi_target(self):
@@ -60,8 +74,8 @@ def test_output_coefsdata_multi_target(self):
         self.assertEqual(coefsdata.Y.shape, (15, 0))
         self.assertEqual(coefsdata.metas.shape, (15, 2))
 
-        attr_names = ["coef (MEDV)", "coef (CRIM)", "coef/X_sd (MEDV)",
-                      "coef/X_sd (CRIM)", "w*c 1", "w*c 2"]
+        attr_names = ["coef (MEDV)", "coef (CRIM)", "coef * X_sd (MEDV)",
+                      "coef * X_sd (CRIM)", "w*c 1", "w*c 2"]
         self.assertEqual(attr_names,
                          [v.name for v in coefsdata.domain.attributes])
         self.assertEqual(["Variable name", "Variable role"],
@@ -75,8 +89,8 @@ def test_output_coefsdata_multi_target(self):
         self.assertAlmostEqual(coefsdata.X[0, 4], -0.198, 3)
         self.assertAlmostEqual(coefsdata.X[12, 4], -0.288, 3)
         self.assertAlmostEqual(coefsdata.X[13, 4], 0.243, 3)
-        self.assertAlmostEqual(coefsdata.X[-1, 0], 22.5, 1)
-        self.assertAlmostEqual(coefsdata.X[-1, 1], 3.6, 1)
+        self.assertAlmostEqual(coefsdata.X[-1, 0], 6.7, 1)
+        self.assertAlmostEqual(coefsdata.X[-1, 1], -12.2, 1)
         self.assertTrue(np.isnan(coefsdata.X[-1, 4:]).all())
 
     def test_output_data(self):

requirements-core.txt

@@ -18,7 +18,7 @@ pip>=19.3
 python-louvain>=0.13
 pyyaml
 requests
-scikit-learn>=1.4.0
+scikit-learn>=1.5.1
 scipy>=1.9
 serverfiles		# for Data Sets synchronization
 xgboost>=1.7.4,<2.1